Methane is a powerful greenhouse gas, and atmospheric concentrations have risen 2.5 times since the beginning of the Industrial age. While much of this increase is attributed to anthropogenic sources, natural sources, which contribute between 35% and 50% of global methane emissions, are thought to have a role in the atmospheric methane increase, in part due to human influences. Methane emissions from many natural sources are sensitive to climate, and positive feedbacks from climate change and cultural eutrophication may promote increased emissions to the atmosphere. These natural sources include aquatic environments such as wetlands, freshwater lakes, streams and rivers, and estuarine, coastal, and marine systems. Furthermore, there are significant marine sediment stores of methane in the form of clathrates that are vulnerable to mobilization and release to the atmosphere from climate feedbacks, and subsurface thermogenic gas which in exceptional cases may be released following accidents and disasters (North Sea blowout and Deepwater Horizon Spill respectively). Understanding of natural sources, key processes, and controls on emission is continually evolving as new measurement and modeling capabilities develop, and different sources and processes are revealed. This special issue of Limnology and Oceanography gathers together diverse studies on methane production, consumption, and emissions from freshwater, estuarine, and marine systems, and provides a broad view of the current science on methane dynamics of aquatic ecosystems. Here, we provide a general overview of aquatic methane sources, their contribution to the global methane budget, and key uncertainties. We then briefly summarize the contributions to and highlights of this special issue.

An estimated three million shipwrecks exist worldwide and are recognized as cultural resources and foci of archaeological investigations. Shipwrecks also support ecological resources by providing underwater habitats that can be colonized by diverse organisms ranging from microbes to megafauna. In the present article, we review the emerging ecological subdiscipline of shipwreck ecology, which aims to understand ecological functions and processes that occur on shipwrecks. We synthesize how shipwrecks create habitat for biota across multiple trophic levels and then describe how fundamental ecological functions and processes, including succession, zonation, connectivity, energy flow, disturbance, and habitat degradation, manifest on shipwrecks. We highlight future directions in shipwreck ecology that are ripe for exploration, placing a particular emphasis on how shipwrecks may serve as experimental networks to address long-standing ecological questions.

Exposure to oil from the Deepwater Horizon spill may have lasting impacts on preservation of historic shipwrecks in the Gulf of Mexico. Submerged steel structures, including shipwrecks, serve as artificial reefs and become hotspots of biodiversity in the deep sea. Marine biofilms on submerged structures support settlement of micro- and macro-biota and may enhance and protect against corrosion. Disruptions in the local environment, including oil spills, may impact the role that biofilms play in reef preservation. To determine how the Deepwater Horizon spill potentially impacted shipwreck biofilms and the functional roles of the biofilm microbiome, experiments containing carbon steels disks (CSDs) were placed at five historic shipwreck sites located within, and external to the benthic footprint of the Deepwater Horizon spill. The CSDs were incubated for 16 weeks to enable colonization by biofilm-forming microorganisms and to provide time for in situ corrosion to occur. Biofilms from the CSDs, as well as sediment and water microbiomes, were collected and analyzed by 16S rRNA amplicon gene sequencing to describe community composition and determine the source of taxa colonizing biofilms. Biofilm metagenomes were sequenced to compare differential gene abundances at spill-impacted and reference sites. Biofilms were dominated by Zeta-, Alpha-, Epsilon-, and Gamma-proteobacteria. Sequences affiliated with the Mariprofundus and Sulfurimonas genera were prolific, and Roseobacter, and Colwellia genera were also abundant. Analysis of 16S rRNA sequences from sediment, water, and biofilms revealed sediment to be the main known source of taxa to biofilms at impacted sites. Differential gene abundance analysis revealed the two-component response regulator CreC, a gene involved in environmental stress response, to be elevated at reference sites compared to impacted sites within the spill plume fallout area on the seafloor. Genes for chemotaxis, motility, and alcohol dehydrogenases were differentially abundant at reference vs. impacted sites. Metal loss on CSDs was elevated at sites within the spill fallout plume. Time series images reveal that metal loss at a heavily impacted site, the German Submarine U-166, has accelerated since the spill in 2010. This study provides evidence that spill residues on the seafloor may impact biofilm communities and the preservation of historic steel shipwrecks.

Biogeography of macro- and micro-organisms in the deep sea is, in part, shaped by naturally occurring heterogeneous habitat features of geological and biological origin such as seeps, vents, seamounts, whale and wood-falls. Artificial features including shipwrecks and energy infrastructure shape the biogeographic patterns of macro-organisms; how they influence microorganisms is unclear. Shipwrecks may function as islands of biodiversity for microbiomes, creating a patchwork of habitats with influence radiating out into the seabed. Here we show microbiome richness and diversity increase as a function of proximity to the historic deep-sea shipwreck Anona in the Gulf of Mexico. Diversity and richness extinction plots provide evidence of an island effect on microbiomes. A halo of core taxa on the seabed was observed up to 200 m away from the wreck indicative of the transition zone from shipwreck habitat to the surrounding environment. Transition zones around natural habitat features are often small in area compared to what was observed at Anona indicating shipwrecks may exert a large sphere of influence on seabed microbiomes. Historic shipwrecks are abundant, isolated habitats with global distribution, providing a means to explore contemporary processes shaping biogeography on the seafloor. This work is a case study for how built environments impact microbial biodiversity and provides new information on how arrival of material to the seafloor shapes benthic microbiomes.

More than 2,000 historic shipwrecks spanning 500 years of history, rest on the Gulf of Mexico seafloor. Shipwrecks serve as artificial reefs and hotspots of biodiversity by providing hard substrate, something rare in deep ocean regions. The Deepwater Horizon (DWH) spill discharged crude oil into the deep Gulf. Because of physical, biological, and chemical interactions, DWH oil was deposited on the seafloor, where historic shipwrecks are present. This study examined sediment microbiomes at seven historic shipwrecks. Steel-hulled, World War II-era shipwrecks and wooden-hulled, 19^th century shipwrecks within and outside of the surface oiled area and subsurface plume were examined. Analysis of 16S rRNA sequence libraries, sediment radiocarbon age data, sedimentation rates, and hydrocarbons revealed that the German U-boat U-166 and the wooden-hulled sailing vessel known as the Mardi Gras Wreck, both in the Mississippi Canyon leasing area, were exposed to deposited oil during a rapid sedimentation event. Impacts to shipwreck microbiomes included a significant increase in Piscirickettsiaceae-related sequences in surface sediments, and reduced biodiversity relative to unimpacted sites. This study is the first to address the impact of the spill on shipwreck-associated microbiomes, and to explore how shipwrecks themselves influence microbiome diversity in the deep sea.

The release of hydrocarbons and chemical dispersant in marine environments may disrupt benthic ecosystems, including artificial reefs, formed by historic steel shipwrecks, and their associated organisms. Experiments were performed to determine the impacts of crude oil, dispersed crude oil, and dispersant on the community structure and function of microorganisms in seawater (SW) and biofilms formed on carbon steel, a common ship hull construction material. Steel corrosion was also monitored to illustrate how oil spills may impact preservation of steel shipwrecks. Microcosms were filled with seawater (SW) and incubated at 4°C. Carbon steel disks (CSDs) were placed in each tank, and tanks were amended with crude oil and/or dispersant or no treatment. SW and CSD biofilms were sampled biweekly for genetic analysis using Illumina sequencing of 16S ribosomal RNA gene amplicons. Predicted and sequenced bacterial metagenomes were analyzed to examine impacts of oil and dispersant on metabolic function. Gammaproteobacteria, Alphaproteobacteria, and Flavobacteriia dominated SW and biofilms. Bacterial community structure differed significantly between treatments for SW and biofilms. OTUs affiliated with known (Pseudomonas) and potential (Marinomonas) hydrocarbon-degraders were roughly twice as abundant in biofilms treated with oil and dispersed oil, and steel corrosion of CSDs in these treatments was higher compared to control and dispersant treatments. OTUs affiliated with the Rhodobacteraceae family (biofilm formers and potential oil degraders) were less abundant in the dispersant treatment compared to other treatments in biofilm and SW samples, but OTUs affiliated with the Pseudoalteromonas genus (biofilm formers and proposed hydrocarbon degraders) were more abundant in dispersant-treated biofilms. Overall, functional gene analyses revealed a decrease in genes (predicted using PICRUSt and observed in sequenced metagenomes) associated with hydrocarbon degradation in dispersant-treated biofilms. This study indicates that exposure to oil and dispersant could disrupt the composition and metabolic function of biofilms colonizing metal hulls, as well as corrosion processes, potentially compromising shipwrecks as ecological and historical resources.