S. Emil Ruff

Marine Biological Laboratory | MBL · Josephine Bay Paul Center for Comparative Molecular Biology and Evolution

Significance Methane seeps are natural gas leaks at the seafloor that emit methane to the hydrosphere. The emission rates are controlled by methane-oxidizing microorganisms, which shape the ecosystem by supplying energy sources to other microorganisms and animal symbioses. We provide evidence that methane seeps are island-like habitats, harboring d...

The methane-emitting cold seeps of Hikurangi margin (New Zealand) are among the few deep-sea chemosynthetic ecosystems of the Southern Hemisphere known to date. Here we compared the biogeochemistry and microbial communities of a variety of Hikurangi cold seep ecosystems. These included highly reduced seep habitats dominated by bacterial mats, parti...

The anaerobic oxidation of methane (AOM) is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), and has mainly been investigated in deep-sea sediments. Here we studied methane seepage...

In marine sediments the anaerobic oxidation of methane with sulfate as electron acceptor (AOM) is responsible for the removal of a major part of the greenhouse gas methane. AOM is performed by consortia of anaerobic methane-oxidizing archaea (ANME) and their specific partner bacteria. The physiology of these organisms is poorly understood, which is...

Hydrothermal sediments host phylogenetically diverse and physiologically complex microbial communities. Previous studies of microbial community structure in hydrothermal sediments have typically used short-read sequencing approaches. To improve on these approaches, we use LoopSeq, a high-throughput synthetic long-read sequencing method that has yie...

Subsurface environments are among Earth’s largest habitats for microbial life. Yet, until recently, we lacked adequate data to accurately differentiate between globally distributed marine and terrestrial surface and subsurface microbiomes. Here, we analyzed 478 archaeal and 964 bacterial metabarcoding datasets and 147 metagenomes from diverse and w...

Over the past decade, sequencing data generated by large microbiome projects showed that taxa exhibit patchy geographical distribution, raising questions about the geospatial dynamics that shape natural microbiomes and the spread of antimicrobial resistance (AMR) genes. Answering these questions requires distinguishing between local and non-local m...

Nearly all molecular oxygen (O2) on Earth is produced via oxygenic photosynthesis by plants or photosynthetically active microorganisms. Light-independent O2 production, which occurs both abiotically, e.g., through water radiolysis, or biotically, e.g., through the dismutation of nitric oxide or chlorite, has been thought to be negligible to the Ea...

The 72‐foot sailing yacht Eugen Seibold is a new research platform for contamination‐free sampling of the water column and atmosphere for biological, chemical, and physical properties, and the exchange processes between the two realms. Ultimate goal of the project is a better understanding of the modern and past ocean and climate. Operations starte...

The photodegradation of macroplastics in the marine environment remains poorly understood. Here, we investigated the weathering of commercially available plastics (tabs 1.3 × 4.4 × 0.16 cm), including high-density polyethylene, low-density polyethylene, polypropylene, polystyrene, and poly-carbonate, in seawater under laboratory-simulated ultraviol...

Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use mul...

Nitrogen bioavailability, governed by the balance of fixation and loss processes, is a key factor regulating oceanic productivity, ecosystem functions, and global biogeochemical cycles. The key nitrogen-loss organisms—denitrifiers and anaerobic ammonium-oxidizing (anammox) bacteria—are not well understood in marine seafloor environments, especially...

Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved but understudied ANME group, 'Candidatus Methanovorans' (ANME-3) to identify evolutionary processes and innovati...

Hydrothermal vents host phylogenetically diverse and physiologically complex microbial communities. Previous studies of microbial community structure in hydrothermal sediments have typically used short-read sequencing approaches. To address these shortcomings, we use LoopSeq, a high-throughput synthetic long-read sequencing method that has yielded...

Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use mul...

The photodegradation of macroplastics in the marine environment remains poorly understood. Here we investigated the weathering of commercially available plastics (tabs 1.3 x 4.4 x 0.16 cm), including high-density polyethylene (HDPE), low-density polyethylene (LDPE), polypropylene (PP), polystyrene (PS), and polycarbonate (PC), in seawater under lab...

Sulfur-cycling microbial communities in salt marsh rhizosphere sediments mediate a recycling and detoxification system central to plant productivity. Despite the importance of sulfur-cycling microbes, their biogeographic, phylogenetic, and functional diversity remain poorly understood. Here, we use metagenomic data sets from Massachusetts (MA) and...

Around 50% of humankind relies on groundwater as a source of drinking water. We investigated the age, geochemistry, and microbiology of 138 groundwater samples from 87 monitoring wells (<250 m depth) located in 14 aquifers in Canada (Fig. 1). Geochemistry and microbiology showed consistent trends suggesting large-scale aerobic and anaerobic hydroge...

Marine and terrestrial subsurface sediments, rocks, and water may represent the largest habitat for microbial life on Earth. Despite the global importance of subsurface ecosystems for biogeochemical cycling and microbial diversity, essential questions remain unanswered. These concern the abundance of novel microbial clades in the subsurface, the di...

Introduction The ancient city of Tel Megiddo in the Jezreel Valley (Israel), which lasted from the Neolithic to the Iron Age, has been continuously excavated since 1903 and is now recognized as a World Heritage Site. The site features multiple ruins in various areas, including temples and stables, alongside modern constructions, and public access i...

Around 50% of humankind relies on groundwater as a source of drinking water. Here we investigate the age, geochemistry, and microbiology of 138 groundwater samples from 95 monitoring wells (<250 m depth) located in 14 aquifers in Canada. The geochemistry and microbiology show consistent trends suggesting large-scale aerobic and anaerobic hydrogen,...

Sulfur-oxidizing and sulfate-reducing bacteria in salt marsh sediments are major controllers of ecosystem-scale carbon cycling. Cross-site comparisons of S-cycling communities are difficult given the rampant uncultured microbial diversity in sediment, yet comparisons are essential for revealing biogeographic, phylogenetic and functionally significa...

Marine cold seeps are unique chemosynthetic habitats fueled by deeply sourced hydrocarbon-rich fluids discharged at the seafloor. Through oxidizing methane and other hydrocarbons, microorganisms inhabiting cold seeps supply subsurface-derived energy to higher trophic levels, sustaining highly productive oases of life in the deep sea. Despite the ce...

Marine cold seeps are unique chemosynthetic habitats fueled by deeply sourced hydrocarbon‐rich fluids discharged at the seafloor. Through oxidizing methane and other hydrocarbons, microorganisms inhabiting cold seeps supply subsurface‐derived energy to higher trophic levels, sustaining highly productive oases of life in the deep sea. Despite the ce...

Groundwater ecosystems are globally widespread yet still poorly understood. We investigated the age, aqueous geochemistry, and microbiology of 138 groundwater samples from 87 monitoring wells (<250m depth) located in 14 aquifers in the Canadian Prairie. Geochemistry and microbial ecology were tightly linked revealing large-scale aerobic and anaerob...

The anthozoan sea anemone Nematostella vectensis belongs to the phylum of cnidarians which also includes jellyfish and corals. Nematostella are native to United States East Coast marsh lands, where they constantly adapt to changes in salinity, temperature, oxygen concentration and pH. Its natural ability to continually acclimate to changing environ...

Hydrothermal sediments contain large numbers of uncultured heterotrophic microbial lineages. Here, we amended Guaymas Basin sediments with proteins, polysaccharides, nucleic acids or lipids under different redox conditions and cultivated heterotrophic thermophiles with the genomic potential for macromolecule degradation. We reconstructed 20 metagen...

Cold seeps and hydrothermal vents are seafloor habitats fueled by subsurface energy sources. Both habitat types coexist in Guaymas Basin in the Gulf of California, providing an opportunity to compare microbial communities with distinct physiologies adapted to different thermal regimes. Hydrothermally active sites in the southern Guaymas Basin axial...

The Amazon rainforest is theworld's largest tropical forest, and this biomemay be a significant contributor to primary biological aerosol (PBA) emissions on a global scale. These aerosols also play a pivotal role in modulating ecosystem dynamics, dispersing biological material over geographic barriers and influencing climate through radiation absor...

Methyl‐coenzyme M reductase (MCR) has been originally identified to catalyze the final step of the methanogenesis pathway. About 20 years ago anaerobic methane‐oxidizing archaea (ANME) were discovered that use MCR enzymes to activate methane. ANME thrive at the thermodynamic limit of life, are slow‐growing, and in most cases form syntrophic consort...

Marine cold seeps transmit fluids between the subseafloor and seafloor biospheres through upward migration of hydrocarbons that originate in deep sediment layers. It remains unclear how geofluids influence the composition of the seabed microbiome and if they transport deep subsurface life up to the surface. Here we analyzed 172 marine surficial sed...

Supplementary Information for Chakraborty et al. PNAS 2020

Hydrocarbon seeps are common features of all oceans and are located mainly along the continental margins (Fig. 1). Seeps are locally restricted, yet highly productive hotspots of biodiversity that experience very different environmental conditions and energy regimes than the surrounding deep-sea sediments. Hydrocarbon seep ecosystems are mostly fue...

Extraction of natural gas from unconventional hydrocarbon reservoirs by hydraulic fracturing raises concerns about methane migration into groundwater. Microbial methane oxidation can be a significant methane sink. Here, we inoculated replicated, sand-packed, continuous mesocosms with groundwater from a field methane release experiment. The mesocosm...

Background Lagoons are common along coastlines worldwide and are important for biogeochemical element cycling, coastal biodiversity, coastal erosion protection and blue carbon sequestration. These ecosystems are frequently disturbed by weather, tides, and human activities. Here, we investigated a shallow lagoon in New England. The brackish ecosyste...

Dormant endospores of anaerobic, thermophilic bacteria found in cold marine sediments offer a useful model for studying microbial biogeography, dispersal, and survival. The dormant endospore phenotype confers resistance to unfavorable environmental conditions, allowing dispersal to be isolated and studied independently of other factors such as envi...

Phototrophic microbial mats commonly contain multiple phototrophic lineages that coexist based on their light, oxygen and nutrient preferences. Here we show that similar coexistence patterns and ecological niches can occur in suspended phototrophic blooms of an organic-rich estuary. The water column showed steep gradients of oxygen, pH, sulfate, su...

Emission of the greenhouse gas methane from the seabed is globally controlled by marine aerobic and anaerobic methanotrophs gaining energy via methane oxidation. However, the processes involved in the assembly and dynamics of methanotrophic populations in complex natural microbial communities remain unclear. Here we investigated the development of...

Fig. S1. Visualization of assembled contigs of the six metagenomes (Oxy‐1, Oxy‐2, Nit‐1, Nit‐2, Con‐1, Con‐2) after binning. Bins A‐R are indicated with capital letters. Letters in parentheses show large bins that were detected, but had assembled better in another sample. Refer to this graph to link the metatranscriptomic contig identifier (Dataset...

For the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate-reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investiga...

For the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate-reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investiga...

Expansion of shale gas extraction has fuelled global concern about the potential impact of fugitive methane on groundwater and climate. Although methane leakage from wells is well documented, the consequences on groundwater remain sparsely studied and are thought by some to be minor. Here we present the results of a 72-day methane gas injection exp...

Concerns over potential environmental impacts of shale gas extraction using e.g. hydraulic fracturing, have raised questions regarding the vulnerability of shallow aquifers to fugitive methane (CH4) contamination. How do in situ microbial communities respond to the presence of fugitive methane in groundwater? To what extent does the availability of...

The expansion of unconventional natural gas extraction (e.g. from shale) has raised concerns over potential impacts of fugitive methane migration on shallow groundwater. To provide direct insight into the effect of methane (CH4) and the microbial processes involved in CH4 removal from contaminated aquifers, we performed metagenomic and microbiologi...

The anaerobic oxidation of methane (AOM) is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), and has mainly been investigated in deep-sea sediments. Here we studied methane seepage...

The hydrothermal sediments of Guaymas Basin, an active spreading center in the Gulf of California (Mexico), are rich in porewater methane, short-chain alkanes, sulfate and sulfide, and provide a model system to explore habitat preferences of microorganisms, including sulfate-dependent, methane- and short chain alkane-oxidizing microbial communities...