Methyl-Based Methanogenesis: an Ecological and Genomic Review

Methyl-based methanogenesis is one of three broad categories of archaeal anaerobic methanogenesis, including both the methyl dismutation (methylotrophic) pathway and the methyl-reducing (also known as hydrogen-dependent methylotrophic) pathway. Methyl-based methanogenesis is increasingly recognized as an important source of methane in a variety of environments. Here, we provide an overview of methyl-based methanogenesis research, including the conditions under which methyl-based methanogenesis can be a dominant source of methane emissions, experimental methods for distinguishing different pathways of methane production, molecular details of the biochemical pathways involved, and the genes and organisms involved in these processes. We also identify the current gaps in knowledge and present a genomic and metagenomic survey of methyl-based methanogenesis genes, highlighting the diversity of methyl-based methanogens at multiple taxonomic levels and the widespread distribution of known methyl-based methanogenesis genes and families across different environments.

Limited underthrusting of India below Tibet: 3He/4He analysis of thermal springs locates the mantle suture in continental collision

Our regional-scale geochemical dataset (³He/⁴He) resolves the geometry of the continental collision between India and Asia. Geophysical images have led to contradictory interpretations that India directly underthrusts Tibet as a horizontal plate or India subducts steeply into the mantle. Helium transits from mantle depths to the surface within a few millennia, such that the ratio of mantle-derived ³He to dominantly crust-derived ⁴He provides a snapshot of the subsurface. ³He/⁴He data from 225 geothermal springs across a >1,000-km-wide region of southern Tibet define a sharp boundary subparallel to the surface suture between India and Asia, just north of the Himalaya, delineating the northern limit of India at ∼80-km depth. The India–Asia collision resembles oceanic subduction with an asthenospheric mantle wedge.

During continent–continent collision, does the downgoing continental plate underplate far inboard of the collisional boundary or does it subduct steeply into the mantle, and how is this geometry manifested in the mantle flow field? We test conflicting models for these questions for Earth’s archetypal continental collision forming the Himalaya and Tibetan Plateau. Air-corrected helium isotope data (³He/⁴He) from 225 geothermal springs (196 from our group, 29 from the literature) delineate a boundary separating a Himalayan domain of only crustal helium from a Tibetan domain with significant mantle helium. This 1,000-km-long boundary is located close to the Yarlung-Zangbo Suture (YZS) in southern Tibet from 80 to 92°E and is interpreted to overlie the “mantle suture” where cold underplated Indian lithosphere is juxtaposed at >80 km depth against a sub-Tibetan incipiently molten asthenospheric mantle wedge. In southeastern Tibet, the mantle suture lies 100 km south of the YZS, implying delamination of the mantle lithosphere from the Indian crust. This helium-isotopic boundary helps resolve multiple, mutually conflicting seismological interpretations. Our synthesis of the combined data locates the northern limit of Indian underplating beneath Tibet, where the Indian plate bends to steeper dips or breaks off beneath a (likely thin) asthenospheric wedge below Tibetan crust, thereby defining limited underthrusting for the Tibetan continental collision.

The Use of Noble Gas Isotopes in Detecting Methane Contamination of Groundwater in Shale Gas Development Areas: An Overview of Technology and Methods

Groundwater contamination by stray gas (mainly methane) in areas of shale-gas development has captured publics, political and scientific attention. However, the sources and potential mechanisms of groundwater contamination are still debated. Noble gases can provide useful information on fluid migration for discerning the scale, conditions, and physical mechanisms. In this study, details about analytical technology and theoretical approach of noble gases in tracing groundwater contaminations are presented. In addition, applications of noble-gases isotopes for determining contamination sources and potential pathways are explored and reviewed. Recent developments are discussed and highlighted with focusing on new utilities of noble-gas isotope parameters in evaluating groundwater contamination. Some usages of indicators (⁴He/²⁰Ne, CH₄/³⁶Ar, ⁴He/CH₄, etc.) are discussed through specific research articles. And it is a new trend to make comprehensive use of multiple geochemical parameters to determine the occurrence, source, and process of methane pollution in groundwater.

Members of Marinobacter and Arcobacter Influence System Biogeochemistry During Early Production of Hydraulically Fractured Natural Gas Wells in the Appalachian Basin

Hydraulic fracturing is the prevailing method for enhancing recovery of hydrocarbon resources from unconventional shale formations, yet little is understood regarding the microbial impact on biogeochemical cycling in natural-gas wells. Although the metabolisms of certain fermentative bacteria and methanogenic archaea that dominate in later produced fluids have been well studied, few details have been reported on microorganisms prevelant during the early flowback period, when oxygen and other surface-derived oxyanions and nutrients become depleted. Here, we report the isolation, genomic and phenotypic characterization of Marinobacter and Arcobacter bacterial species from natural-gas wells in the Utica-Point Pleasant and Marcellus Formations coupled to supporting geochemical and metagenomic analyses of produced fluid samples. These unconventional hydrocarbon system-derived Marinobacter sp. are capable of utilizing a diversity of organic carbon sources including aliphatic and aromatic hydrocarbons, amino acids, and carboxylic acids. Marinobacter and Arcobacter can metabolize organic nitrogen sources and have the capacity for denitrification and dissimilatory nitrate reduction to ammonia (DNRA) respectively; with DNRA and ammonification processes partially explaining high concentrations of ammonia measured in produced fluids. Arcobacter is capable of chemosynthetic sulfur oxidation, which could fuel metabolic processes for other heterotrophic, fermentative, or sulfate-reducing community members. Our analysis revealed mechanisms for growth of these taxa across a broad range of salinities (up to 15% salt), which explains their enrichment during early natural-gas production. These results demonstrate the prevalence of Marinobacter and Arcobacter during a key maturation phase of hydraulically fractured natural-gas wells, and highlight the significant role these genera play in biogeochemical cycling for this economically important energy system.

Hydrocarbon-Rich Groundwater above Shale-Gas Formations: A Karoo Basin Case Study

Horizontal drilling and hydraulic fracturing have enhanced unconventional hydrocarbon recovery but raised environmental concerns related to water quality. Because most basins targeted for shale-gas development in the USA have histories of both active and legacy petroleum extraction, confusion about the hydrogeological context of naturally occurring methane in shallow aquifers overlying shales remains. The Karoo Basin, located in South Africa, provides a near-pristine setting to evaluate these processes, without a history of conventional or unconventional energy extraction. We conducted a comprehensive pre-industrial evaluation of water quality and gas geochemistry in 22 groundwater samples across the Karoo Basin, including dissolved ions, water isotopes, hydrocarbon molecular and isotopic composition, and noble gases. Methane-rich samples were associated with high-salinity, NaCl-type groundwater and elevated levels of ethane, ⁴ He, and other noble gases produced by radioactive decay. This endmember displayed less negative δ¹³ C-CH₄ and evidence of mixing between thermogenic natural gases and hydrogenotrophic methane. Atmospheric noble gases in the methane-rich samples record a history of fractionation during gas-phase migration from source rocks to shallow aquifers. Conversely, methane-poor samples have a paucity of ethane and ⁴ He, near saturation levels of atmospheric noble gases, and more negative δ¹³ C-CH₄ ; methane in these samples is biogenic and produced by a mixture of hydrogenotrophic and acetoclastic sources. These geochemical observations are consistent with other basins targeted for unconventional energy extraction in the USA and contribute to a growing data base of naturally occurring methane in shallow aquifers globally, which provide a framework for evaluating environmental concerns related to unconventional energy development (e.g., stray gas).