Guaymas Basin Research Articles

Deep subseafloor sediments in Guaymas Basin harbor cosmopolitan microbiota and traces of hydrothermal populations

Environmental factors shape subsurface microbial ecosystems, and well-characterized sites are ideal for determining how environmental parameters shape sediment communities. Sediments from eight geologically and thermally distinct sites were drilled during International Ocean Discovery Program Expedition 385 in Guaymas Basin, an expedition focused on the hydrothermal deep biosphere. Using high-throughput 16S ribosomal nucleic acid sequencing, cell counts, phylogenetics, metatranscriptomics, and mineralogical/elemental X-ray spectroscopy, we examine linkages and feedbacks between mineral composition, temperature, geochemistry, and microbial populations. We show subsurface life is dominated by heterotrophic, cosmopolitan prokaryotes that thrive within a range of sediments and temperature conditions across Guaymas Basin. Hydrothermally-affiliated lineages are detected in low numbers at sites with steepest temperature gradients, within communities of mesophilic taxa that occur throughout Guaymas Basin and in other marine subsurface habitats. Thus, hydrothermal lineages do not replace the cosmopolitan, mesophilic subsurface community, but remain specific to sites where volcanic intrusions drive hydrothermal circulation.

Microbial anabolic and catabolic utilization of hydrocarbons in deep subseafloor sediments of Guaymas Basin.

Guaymas Basin, located in the Gulf of California, is a hydrothermally active marginal basin. Due to steep geothermal gradients and localized heating by sill intrusions, microbial substrates like short-chain fatty acids and hydrocarbons are abiotically produced from sedimentary organic matter at comparatively shallow depths. We analyzed the effect of hydrocarbons on uptake of hydrocarbons by microorganisms via nano-scale secondary ion mass spectrometry (NanoSIMS) and microbial sulfate reduction rates (SRR), using samples from two drill sites sampled by IODP Expedition 385 (U1545C and U1546D). These sites are in close proximity of each other (ca. 1km) and have very similar sedimentology. Site U1546D experienced the intrusion of a sill that has since then thermally equilibrated with the surrounding sediment. Both sites currently have an identical geothermal gradient, despite their different thermal history. The localized heating by the sill led to thermal cracking of sedimentary organic matter and formation of potentially bioavailable organic substrates. There were low levels of hydrocarbon and nitrogen uptake in some samples from both sites, mostly in surficial samples. Hydrocarbon and methane additions stimulated SRR in near-seafloor samples from Site U1545C, while samples from Site U1546D reacted positively only on methane. Our data indicate the potential of microorganisms to metabolize hydrocarbons even in the deep subsurface of Guaymas Basin.

Impacts of temperature and fluid seepage on organic matter composition in sediments of an active hydrothermal basin

Marine sediments are one of the largest organic carbon (OC) sinks on Earth. Yet, major knowledge gaps remain in our understanding of sedimentary OC cycling, particularly regarding temperature-induced alteration processes of OC from different sources. Here, we investigate OC-rich sediments of Guaymas Basin (Gulf of California) across two hydrothermal areas, one with only conductive geothermal heating and the other additionally experiencing seepage of hydrocarbon-rich fluids from deeper layers. We use Pyrolysis-Gas Chromatography/Mass Spectrometry (Py-GC/MS) to investigate diagenetic OC changes and show that cold control sites in both hydrothermal areas are dominated by similar contributions of lipid-derived compounds, nitrogenous (likely protein-derived) compounds, carbohydrates, and polyaromatic hydrocarbons (PAHs). These OC compound groups are largely derived from phytoplankton detritus from overlying water. Conductively heated sediments, which reach in situ temperatures of ∼ 80 °C, have similar general OC compositions and contents to these cold sites, but show evidence of diagenetic modifications of individual carbohydrate groups in deeper layers. By contrast, strong decreases in carbohydrate and nitrogenous compound abundances at the seep sites indicate that these compound groups are not only modified but also selectively degraded at the higher temperatures (>80 °C) of these sites. Increases in pyrolysis products of PAHs, prist-1-ene, and alkanes with depth, moreover, show that import of OC by deep hydrothermal fluids contributes significantly to sedimentary OC pools mainly in deeper layers of these sites. Our study provides the first comprehensive analysis of major OC compound groups in Guaymas Basin sediment and indicates that the supply of OC by hydrothermal fluid flow only has minor impacts on particulate organic matter compositions at the seafloor, even at active seep sites. We furthermore show that temperatures up to ∼ 80 °C already result in thermochemical modifications of organic matter (OM) that are potentially linked to the onset of kerogen formation. The sequence and time scales of chemical modifications and activations in relation to temperature are an important subject for future investigations.

Single-cell analysis reveals an active and heterotrophic microbiome in the Guaymas Basin deep subsurface with significant inorganic carbon fixation by heterotrophs.

The global subsurface is the largest reservoir of microbial life on the planet yet remains poorly characterized. The activity of life in this realm has implications for long-term elemental cycling, particularly of carbon, as well as how life survives in extreme environments. Here, we recovered cells from the deep subsurface of the Guaymas Basin and investigated the level and distribution of microbial activity, the physicochemical drivers of activity, and the relative significance of organic versus inorganic carbon to subsurface biomass. Using a sensitive single-cell assay, we found that the majority of cells are active, that activity is likely driven by the availability of energy, and that although heterotrophy is the dominant metabolism, both organic and inorganic carbon are used to generate biomass. Using a new approach, we quantified inorganic carbon assimilation by heterotrophs and highlighted the importance of this often-overlooked mode of carbon assimilation in the subsurface and beyond.

Nitrogen isotope homogenization of dissolved ammonium with depth and 15N enrichment of ammonium during incorporation into expandable layer silicates in organic-rich marine sediment from Guaymas Basin, Gulf of California

Sedimentary nitrogen isotopic ratios are used as a proxy for ancient biogeochemical cycles on Earth's surface. It is generally accepted that sediment hole tops record primary signatures because organic nitrogen (ON) is predominant in this part of the hole. In contrast to such early to middle diagenetic stages, it is well known that heavier nitrogen isotope 15N tends to enrich in sedimentary rocks during later diagenetic and metamorphic stages. However, there are some critical gaps in our understanding of nitrogen isotopic alteration associated with abiotic processes during early-middle diagenesis. In this study, we examined the isotope ratios of ammonium nitrogen in interstitial water (IW) and total nitrogen (TN), including exchangeable ammonium and mineral nitrogen, in the solid-phase of organic-rich-sediment recovered by International Ocean Discovery Program (IODP) Expedition 385 cores drilled in the Guaymas Basin, Gulf of California, that contained ammonium-rich IW. The isotopic ratios (δ15N value) of TN are the most variable with depth compared to any other type of nitrogen. This variation can be interpreted as reflecting changes in the water mass environment in the basin caused by glacial–interglacial climate changes, modifying the δ15N values of the marine primary producers. Thus, the δ15N value of TN is a proxy for environmental change in the basin, while each component of TN shows different trends. The δ15N values of IW and exchangeable ammonium did not exhibit significant changes with depth, but the latter values are about 3 ‰ enriched in 15N. This may be due to advective transport of solute into adjacent layers followed by the formation of an isotopic equilibrium between IW and exchangeable ammonium in the case of fast sediment accumulation rate. The δ15N value of exchangeable ammonium is the highest among the other types of nitrogen with one exception, where the δ15N value of TN is the highest. The calculated δ15N values of ON based on mass balance are almost the same as those of associated TN in the shallow sediment layers (< 150 m below seafloor), but the difference in the δ15N values of TN and ON are significant in the deeper layers, where proportions of ON contents are <50%. In particular, in the layer where the δ15N value of TN is the highest, that of ON shows an even higher value and the difference reaches 3.5 ‰. The δ15N values of mineral nitrogen are similar to that of IW ammonium except the surface layers. Under such conditions, when δ15N value of TN is intermediate between those of mineral nitrogen and exchangeable ammonium, calculated δ15N value of ON is close to that of TN. On the other hand, if δ15N value of TN is out of the range between mineral nitrogen and exchangeable ammonium, it causes further difference in δ15N value of ON. It means that the fluctuation of δ15N values of TN is reduced relative to those of ON through depth. It has been considered that δ15N value of TN in sediment is similar to that of ON, and changes in the δ15N value of TN due to diagenesis are limited, but in such environment ON fluctuations over depth may be slightly underestimated.

Evolution of ocean circulation and water masses in the Guaymas Basin (Gulf of California) during the last 31,000 years revealed by radiolarians and silicoflagellates in IODP expedition 385 sediment cores

The high-resolution analysis of radiolarians and silicoflagellates in sediments from Holes U1545A and U1549A drilled during IODP Expedition 385 in the Guaymas Basin, in the Gulf of California provides detailed insights into the evolution of ocean circulation and water masses, and its relation to Eastern Tropical Pacific Ocean climate conditions, over the past 31,000 cal years BP (based on AMS radiocarbon dates). In the pre-Last Glacial Maximum, the Guaymas Basin experienced alternating circulation patterns of California Current Water (CCW) and Gulf of California Water (GCW), with an extended presence of the Pacific Intermediate Water (PIW) owing to: amplified jet streams; southern movement of the California Current System (CCS) and the incursion of CCW into the gulf; and increased North Pacific Intermediate Water (NPIW) formation. The Last Glacial Maximum witnessed the incursion of CCW due to the stronger CCS. The dominance of the PIW indicates the expansion and formation of NPIW. The Heinrich-I event as manifested in the core record, displays two distinct patterns, one suggesting GCW-like dominance and the other, the occurrence of CCW. The Bølling-Ållerød interstadial featured the entry of Tropical Surface Water (TSW), GCW, and CCW, linked with the northward migration of the Intertropical Convergence Zone. In the Younger Dryas, CCW dominated, transitioning to GCW as colder climatic conditions and more intense CCS. The Holocene displayed alternating periods of TSW and GCW, with a modern monsoon regime from 7,600 to 1,000 cal years BP. From 1,000 cal years BP to the present the ITCZ shifted to the south.

Anaerobic hexadecane degradation by a thermophilic Hadarchaeon from Guaymas Basin.

Hadarchaeota inhabit subsurface and hydrothermally heated environments, but previous to this study, they had not been cultured. Based on metagenome-assembled genomes, most Hadarchaeota are heterotrophs that grow on sugars and amino acids, or oxidize carbon monoxide or reduce nitrite to ammonium. A few other metagenome-assembled genomes encode alkyl-coenzyme M reductases (Acrs), β-oxidation, and Wood-Ljungdahl pathways, pointing toward multicarbon alkane metabolism. To identify the organisms involved in thermophilic oil degradation, we established anaerobic sulfate-reducing hexadecane-degrading cultures from hydrothermally heated sediments of the Guaymas Basin. Cultures at 70°C were enriched in one Hadarchaeon that we propose as Candidatus Cerberiarchaeum oleivorans. Genomic and chemical analyses indicate that Ca. C. oleivorans uses an Acr to activate hexadecane to hexadecyl-coenzyme M. A β-oxidation pathway and a tetrahydromethanopterin methyl branch Wood-Ljungdahl (mWL) pathway allow the complete oxidation of hexadecane to CO2. Our results suggest a syntrophic lifestyle with sulfate reducers, as Ca. C. oleivorans lacks a sulfate respiration pathway. Comparative genomics show that Acr, mWL, and β-oxidation are restricted to one family of Hadarchaeota, which we propose as Ca. Cerberiarchaeaceae. Phylogenetic analyses further indicate that the mWL pathway is basal to all Hadarchaeota. By contrast, the carbon monoxide dehydrogenase/acetyl-coenzyme A synthase complex in Ca. Cerberiarchaeaceae was horizontally acquired from Bathyarchaeia. The Acr and β-oxidation genes of Ca. Cerberiarchaeaceae are highly similar to those of other alkane-oxidizing archaea such as Ca. Methanoliparia and Ca. Helarchaeales. Our results support the use of Acrs in the degradation of petroleum alkanes and suggest a role of Hadarchaeota in oil-rich environments.

Changes in productivity in the Guaymas Basin over the last 22,000 years: Insights from coccolithophores in sediments from IODP Site U1549.

Changes in productivity in the Guaymas Basin over the last 22,000 years: Insights from coccolithophores in sediments from IODP Site U1549.

A PCR-Based Survey of Methane-Cycling Archaea in Methane-Soaked Subsurface Sediments of Guaymas Basin, Gulf of California.

The Guaymas Basin in the Gulf of California is characterized by active seafloor spreading, the rapid deposition of organic-rich sediments, steep geothermal gradients, and abundant methane of mixed thermogenic and microbial origin. Subsurface sediment samples from eight drilling sites with distinct geochemical and thermal profiles were selected for DNA extraction and PCR amplification to explore the diversity of methane-cycling archaea in the Guaymas Basin subsurface. We performed PCR amplifications with general (mcrIRD), and ANME-1 specific primers that target the alpha (α) subunit of methyl coenzyme M reductase (mcrA). Diverse ANME-1 lineages associated with anaerobic methane oxidation were detected in seven out of the eight drilling sites, preferentially around the methane-sulfate interface, and in several cases, showed preferences for specific sampling sites. Phylogenetically, most ANME-1 sequences from the Guaymas Basin subsurface were related to marine mud volcanoes, seep sites, and the shallow marine subsurface. The most frequently recovered methanogenic phylotypes were closely affiliated with the hyperthermophilic Methanocaldococcaceae, and found at the hydrothermally influenced Ringvent site. The coolest drilling site, in the northern axial trough of Guaymas Basin, yielded the greatest diversity in methanogen lineages. Our survey indicates the potential for extensive microbial methane cycling within subsurface sediments of Guaymas Basin.

Spatial evolution and temporal stability of hydrothermal processes at sediment-covered spreading centers: Constraints from Guaymas Basin, Gulf of California

The Guaymas Basin, Gulf of California is a hydrothermally active sediment-covered oceanic spreading center in the early stages of rifting. Hot-spring fluids were collected from its southern trough in 1998, 2003, and 2008 and analyzed for the concentration and isotopic composition of organic and inorganic aqueous species to assess subseafloor geochemical processes. Fluids discharged from the seafloor through hydrothermal edifices with measured temperatures of 91 to 317 °C. In general, fluids exiting larger structures were characterized by higher temperatures than fluids venting from smaller structures. Measured pH (25 °C) ranged from 5.7 to 7.1. Endmember fluids were characterized by near-zero concentrations of Mg and SO4, depletions in Na, and enrichments in K, Ca, and Cl relative to seawater, reflecting extensive interaction with sediment during circulation. Thermal maturation of sedimentary organic matter resulted in the addition of abundant ΣNH4+, ΣCO2, CH4, short-chain n-alkanes, and carboxylic acids to solution. Organic compounds added to fluids during recharge pass through high temperature deep-seated reaction zones and reach high levels of thermal maturity while others may be added by entrainment of lower temperature sedimentary pore fluids in hydrothermal upflow zones.The relative abundance of many organic compounds mobilized during hydrothermal alteration is consistent with metastable states of thermodynamic equilibrium that likely record subseafloor temperature conditions. The isotope composition of low molecular weight hydrocarbons and elevated concentrations of dissolved Cl suggest that temperatures may have exceeded the two-phase boundary for seawater and subsequently cooled before discharging at the seafloor. Periods of high temperature fluid-sediment or fluid-rock interaction followed by cooling may provide a mechanism for the aqueous mobilization and concentration of sulfide-forming metals in subseafloor mineral deposits. Fluid compositions have remained constant at the southern trough of Guaymas Basin for at least 26 years, indicating decadal stability in the physical and chemical conditions in subseafloor environments as well as the km-scale regional recharge zones containing unaltered sediment.

Metagenomic profiles of archaea and bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface

Previous studies of microbial communities in subseafloor sediments reported that microbial abundance and diversity decrease with sediment depth and age, and microbes dominating at depth tend to be a subset of the local seafloor community. However, the existence of geographically widespread, subsurface-adapted specialists is also possible. Here, we use metagenomic and metatranscriptomic analyses of the hydrothermally heated, sediment layers of Guaymas Basin (Gulf of California, Mexico) to examine the distribution and activity patterns of bacteria and archaea along thermal, geochemical and cell count gradients. We find that the composition and distribution of metagenome-assembled genomes (MAGs), dominated by numerous lineages of Chloroflexota and Thermoproteota, correlate with biogeochemical parameters as long as temperatures remain moderate, but downcore increasing temperatures beyond ca. 45 ºC override other factors. Consistently, MAG size and diversity decrease with increasing temperature, indicating a downcore winnowing of the subsurface biosphere. By contrast, specific archaeal MAGs within the Thermoproteota and Hadarchaeota increase in relative abundance and in recruitment of transcriptome reads towards deeper, hotter sediments, marking the transition towards a specialized deep, hot biosphere.

Metasomatized mantle source of nascent oceanic crust in the Guaymas Basin, Gulf of California

The geochemical characteristics of nascent oceanic crust play a crucial role in unraveling the mantle dynamics of the initial opening of an ocean. The Gulf of California, located at the East Pacific margin, is one of the best examples of an active and obliquely rifted continental margin. However, the mantle source composition of the nascent oceanic crust in the central part of the Gulf has not yet been comprehensively investigated. Here, we report in situ major and trace element contents as well as BSr isotope compositions for basaltic glass samples from off-axis sills drilled by the International Ocean Discovery Program (IODP) Expedition 385 at Sites U1547 and U1548 in the Guaymas Basin in the central part of the Gulf of California. These glassy samples represent tholeiites and predominantly show trace element patterns akin to those of enriched mid-ocean ridge basalts (E-MORBs) but with distinctive enrichments in Ba and K and depletions in Nb, Ta, and Ti. In addition, these samples have high B contents (3.07–3.67 ppm) with enriched Sr isotopes (87Sr/86Sr = 0.7032–0.7037) and heavy B isotopes (δ11B = −5.52‰ to 1.20‰). The mixing model based on B/Nb values and SrB isotopes shows that the nascent oceanic crust in the Guaymas Basin might be generated through partial melting of a depleted MORB mantle (DMM) source metasomatized by melts from subducted slab materials referring to partially dehydrated sediment and altered oceanic crust components. The magmas in the Gulf of California show a systematic decline in their enrichment in fluid-mobile elements (Ba) and depletion in fluid-immobile elements (Nb, Ta, and Ti) from the northern (e.g., Isla San Luis volcanic center) to the central part (Guaymas Basin) and southward to the mouth (e.g., Alarcón Basin) of the Gulf. This suggests that the enriched (recycled) components in their mantle source were gradually extracted and exhausted during Gulf opening and oceanic crustal accretion that advanced in a northward direction. Our results indicate that the Guaymas Basin magmas were derived from a mantle that was fertilized by subduction components. The subduction signature corroborates the Gulf opening as a process that started in response to long-term oblique convergence at the eastern Pacific plate margin without any influence from a mantle plume. This evolution is different from nascent ocean basins that evolved from intraplate rifting, such as the Red Sea, leading to vastly different mantle source characteristics.

Contact metamorphic reactions and fluid–rock interactions related to magmatic sill intrusion in the Guaymas Basin

Abstract. Igneous basaltic intrusions into young organic-rich sedimentary basins have a major impact not only on the carbon cycle but also on major and trace element transfers between deep and superficial geological reservoirs. The actively rifting Guaymas Basin in the Gulf of California, which was drilled by the International Ocean Discovery Program during Expedition 385, represents the nascent stage of an ocean characterized by siliceous organic-rich sediments (diatom ooze) intruded by a very dense network of basaltic sills. This study focuses on Site U1546 where the relatively high geothermal gradient (over 200 ∘C km−1) induces early diagenetic transformations in both pore waters and sediments, involving sulfide, carbonate and silica. Geochemical and mineralogical characterizations of the sediment at sill contacts indicate that sulfides and silica polymorphs are the main phases impacted by contact metamorphism, being evident by a transition from opal-CT to quartz and pyrite to pyrrhotite, respectively. Mass balance calculations have been used to estimate mass transfers in metamorphic aureoles. In the top contact aureole, predominantly isochemical metamorphism is reflected by the presence of authigenic quartz and disseminated 20–50 µm sized pyrrhotite crystals, filling primary interstitial space, and partial dissolution of detrital feldspar grains. In the bottom contact aureole, quartz and euhedral pyrrhotite crystals occur, which are up to 4 times larger than those at the top contact. Significant metamorphism of sediments is observed in the lower contact aureole, where plagioclase recrystallizes around the detrital feldspars and locally euhedral pyroxenes are included in patches of carbonate cement; this suggests precipitation from carbon-rich fluids at temperatures (T) higher than 300 ∘C. The lower contact aureole also is more enriched in CaO, Na2O, Fe2O3 and trace elements (Cu, As, Zn, etc.) compared to the upper contact. Based on these petrological investigations, a conceptual model of magma–sediment–fluid interaction is proposed distinguishing top and bottom contact processes. Initial contact metamorphism due to sill emplacement is characterized by dehydration reactions in sediments and crystallization of new minerals. It was followed by carbonate precipitation from the released fluids. At a final stage, the temperature re-equilibrated with the geothermal gradient and the rocks were further altered by hydrothermal fluids.

The Guaymas Basin – A hot spot for hydrothermal generation and anaerobic microbial degradation of hydrocarbons

Guaymas Basin is a young marginal rift basin in the Gulf of California characterized by active seafloor spreading, rapid deposition of organic-rich sediments, and steep geothermal gradients where sedimentary organic material of photosynthetic origin turns into hydrocarbons - potential microbial substrates. After introducing the sources of hydrocarbons in the subsurface, this short overview discusses the phylogenetic diversity, temperature range and occurrence patterns of novel alkane-oxidizing bacteria and archaea in the hydrothermal sediments of Guaymas Basin. Many of these alkane-degrading specialists function as syntrophic consortia, where sulfate-reducing bacteria accept electron from methane- or alkane-oxidizing archaea. As a source of metagenomes, enrichments, and cultures of these methodologically and conceptually challenging microorganisms, Guaymas Basin stands out as an indispensable field site that has consistently catalyzed new insights into the microbiology of anaerobic hydrocarbon oxidation and assimilation.

Anabolic and Catabolic Microbial Activity in Hydrocarbon-rich Sediments of Guaymas Basin

Guaymas Basin, located in the Gulf of California, Mexico, is a young marginal ocean basin with high sedimentation rates of &amp;gt;1 mm/year, active seafloor spreading, and steep geothermal gradients in its sediment. It hosts a unique microbial subseafloor biosphere as these conditions lead to thermal cracking of sedimentary organic matter and the production of bioavailable organic carbon compounds and hydrocarbons already at shallow depths. The abundance and diversity of potential microbial substrates raise the question of which substrates are being used for catabolic and anabolic microbial metabolism. We thus analyzed the microbial uptake of hydrocarbons and inorganic nitrogen using nanoscale secondary ion mass spectrometry (NanoSIMS) analysis after incubation with stable-isotope labeled substrates. Incubations were carried out with samples from two International Ocean Discovery Program (IODP) Exp. 385 drill sites. Site U1545 is characterized by undisturbed sedimentary strata and a temperature gradient of 225°C/km, whereas Site U1546 has experienced a sill intrusion at greater depth, below the cored interval. The intrusion led to temporary heating of the sediment, but a temperature gradient of 221°C/km indicates thermal equilibration with the surrounding sediment since sill emplacement. Incubations were carried out with 13C-benzene + 2H-hexadecane + 15NH4Cl or 13C-methane + 15NH4Cl at in-situ temperature (4-62°C) and pressure (25 MPa) for 42 days. Additionally, sulfate reduction rates (SRR) were measured by incubating the samples with four aliphatic hydrocarbons + four aromatic hydrocarbons or methane and radioisotope-labeled 35SO42- for 10 days, also at in-situ temperature and pressure. The NanoSIMS analyses reveal that a few samples showed detectable microbial assimilation of hydrocarbons. Nitrogen was significantly assimilated in some samples incubated with methane. The assimilation mostly occurred in samples from near the seafloor (2 and 44 meter below seafloor (mbsf)). Our results indicate that anaerobic microorganisms in Guaymas Basin take up measurable amounts of hydrocarbons and inorganic nitrogen even in the relatively short incubation time of 42 days. The results of the SRR measurements indicate that a mixture of hydrocarbons and methane increases the SRR in samples from near the seafloor (2 mbsf) and around the sulfate-methane transition zone (44 and 55 mbsf) but not in samples from greater depths. Our results show that anaerobic microorganisms in Guaymas Basin can use hydrocarbons for anabolic and catabolic metabolism in this extreme environment. Given the high abundance of various carbon compounds, nitrogen appears to be a limiting factor for cellular growth.

Potential for the anaerobic oxidation of benzene and naphthalene in thermophilic microorganisms from the Guaymas Basin.

Unsubstituted aromatic hydrocarbons (UAHs) are recalcitrant molecules abundant in crude oil, which is accumulated in subsurface reservoirs and occasionally enters the marine environment through natural seepage or human-caused spillage. The challenging anaerobic degradation of UAHs by microorganisms, in particular under thermophilic conditions, is poorly understood. Here, we established benzene- and naphthalene-degrading cultures under sulfate-reducing conditions at 50°C and 70°C from Guaymas Basin sediments. We investigated the microorganisms in the enrichment cultures and their potential for UAH oxidation through short-read metagenome sequencing and analysis. Dependent on the combination of UAH and temperature, different microorganisms became enriched. A Thermoplasmatota archaeon was abundant in the benzene-degrading culture at 50°C, but catabolic pathways remained elusive, because the archaeon lacked most known genes for benzene degradation. Two novel species of Desulfatiglandales bacteria were strongly enriched in the benzene-degrading culture at 70°C and in the naphthalene-degrading culture at 50°C. Both bacteria encode almost complete pathways for UAH degradation and for downstream degradation. They likely activate benzene via methylation, and naphthalene via direct carboxylation, respectively. The two species constitute the first thermophilic UAH degraders of the Desulfatiglandales. In the naphthalene-degrading culture incubated at 70°C, a Dehalococcoidia bacterium became enriched, which encoded a partial pathway for UAH degradation. Comparison of enriched bacteria with related genomes from environmental samples indicated that pathways for benzene degradation are widely distributed, while thermophily and capacity for naphthalene activation are rare. Our study highlights the capacities of uncultured thermophilic microbes for UAH degradation in petroleum reservoirs and in contaminated environments.

Microbial gene expression in Guaymas Basin subsurface sediments responds to hydrothermal stress and energy limitation.

Analyses of gene expression of subsurface bacteria and archaea provide insights into their physiological adaptations to in situ subsurface conditions. We examined patterns of expressed genes in hydrothermally heated subseafloor sediments with distinct geochemical and thermal regimes in Guaymas Basin, Gulf of California, Mexico. RNA recovery and cell counts declined with sediment depth, however, we obtained metatranscriptomes from eight sites at depths spanning between 0.8 and 101.9 m below seafloor. We describe the metabolic potential of sediment microorganisms, and discuss expressed genes involved in tRNA, mRNA, and rRNA modifications that enable physiological flexibility of bacteria and archaea in the hydrothermal subsurface. Microbial taxa in hydrothermally influenced settings like Guaymas Basin may particularly depend on these catalytic RNA functions since they modulate the activity of cells under elevated temperatures and steep geochemical gradients. Expressed genes for DNA repair, protein maintenance and circadian rhythm were also identified. The concerted interaction of many of these genes may be crucial for microorganisms to survive and to thrive in the Guaymas Basin subsurface biosphere.

Well-hidden methanogenesis in deep, organic-rich sediments of Guaymas Basin

Deep marine sediments (>1mbsf) harbor ~26% of microbial biomass and are the largest reservoir of methane on Earth. Yet, the deep subsurface biosphere and controls on its contribution to methane production remain underexplored. Here, we use a multidisciplinary approach to examine methanogenesis in sediments (down to 295 mbsf) from sites with varying degrees of thermal alteration (none, past, current) at Guaymas Basin (Gulf of California) for the first time. Traditional (13C/12C and D/H) and multiply substituted (13CH3D and 12CH2D2) methane isotope measurements reveal significant proportions of microbial methane at all sites, with the largest signal at the site with past alteration. With depth, relative microbial methane decreases at differing rates between sites. Gibbs energy calculations confirm methanogenesis is exergonic in Guaymas sediments, with methylotrophic pathways consistently yielding more energy than the canonical hydrogenotrophic and acetoclastic pathways. Yet, metagenomic sequencing and cultivation attempts indicate that methanogens are present in low abundance. We find only one methyl-coenzyme M (mcrA) sequence within the entire sequencing dataset. Also, we identify a wide diversity of methyltransferases (mtaB, mttB), but only a few sequences phylogenetically cluster with methylotrophic methanogens. Our results suggest that the microbial methane in the Guaymas subsurface was produced over geologic time by relatively small methanogen populations, which have been variably influenced by thermal sediment alteration. Higher resolution metagenomic sampling may clarify the modern methanogen community. This study highlights the importance of using a multidisciplinary approach to capture microbial influences in dynamic, deep subsurface settings like Guaymas Basin.

Expansion of Armatimonadota through marine sediment sequencing describes two classes with unique ecological roles

Marine sediments comprise one of the largest environments on the planet, and their microbial inhabitants are significant players in global carbon and nutrient cycles. Recent studies using metagenomic techniques have shown the complexity of these communities and identified novel microorganisms from the ocean floor. Here, we obtained 77 metagenome-assembled genomes (MAGs) from the bacterial phylum Armatimonadota in the Guaymas Basin, Gulf of California, and the Bohai Sea, China. These MAGs comprise two previously undescribed classes within Armatimonadota, which we propose naming Hebobacteria and Zipacnadia. They are globally distributed in hypoxic and anoxic environments and are dominant members of deep-sea sediments (up to 1.95% of metagenomic raw reads). The classes described here also have unique metabolic capabilities, possessing pathways to reduce carbon dioxide to acetate via the Wood-Ljungdahl pathway (WLP) and generating energy through the oxidative branch of glycolysis using carbon dioxide as an electron sink, maintaining the redox balance using the WLP. Hebobacteria may also be autotrophic, not previously identified in Armatimonadota. Furthermore, these Armatimonadota may play a role in sulfur and nitrogen cycling, using the intermediate compounds hydroxylamine and sulfite. Description of these MAGs enhances our understanding of diversity and metabolic potential within anoxic habitats worldwide.

Candidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes

Methanogenic and methanotrophic archaea produce and consume the greenhouse gas methane, respectively, using the reversible enzyme methyl-coenzyme M reductase (Mcr). Recently, Mcr variants that can activate multicarbon alkanes have been recovered from archaeal enrichment cultures. These enzymes, called alkyl-coenzyme M reductase (Acrs), are widespread in the environment but remain poorly understood. Here we produced anoxic cultures degrading mid-chain petroleum n-alkanes between pentane (C5) and tetradecane (C14) at 70 °C using oil-rich Guaymas Basin sediments. In these cultures, archaea of the genus Candidatus Alkanophaga activate the alkanes with Acrs and completely oxidize the alkyl groups to CO2. Ca. Alkanophaga form a deep-branching sister clade to the methanotrophs ANME-1 and are closely related to the short-chain alkane oxidizers Ca. Syntrophoarchaeum. Incapable of sulfate reduction, Ca. Alkanophaga shuttle electrons released from alkane oxidation to the sulfate-reducing Ca. Thermodesulfobacterium syntrophicum. These syntrophic consortia are potential key players in petroleum degradation in heated oil reservoirs.