Mussel growth supported by methane as sole carbon and energy source

Changes in community structures and functions of the gut microbiomes of deep-sea cold seep mussels during in situ transplantation experiment

BACKGROUND

Many deep-sea invertebrates largely depend on chemoautotrophic symbionts for energy and nutrition, and some of them have reduced functional digestive tracts. By contrast, deep-sea mussels have a complete digestive system although symbionts in their gills play vital roles in nutrient supply. This digestive system remains functional and can utilise available resources, but the roles and associations among gut microbiomes in these mussels remain unknown. Specifically, how the gut microbiome reacts to environmental change is unclear.

RESULTS

The meta-pathway analysis showed the nutritional and metabolic roles of the deep-sea mussel gut microbiome. Comparative analyses of the gut microbiomes of original and transplanted mussels subjected to environmental change revealed shifts in bacterial communities. Gammaproteobacteria were enriched, whereas Bacteroidetes were slightly depleted. The functional response for the shifted communities was attributed to the acquisition of carbon sources and adjusting the utilisation of ammonia and sulphide. Self-protection was observed after transplantation.

CONCLUSION

This study provides the first metagenomic insights into the community structure and function of the gut microbiome in deep-sea chemosymbiotic mussels and their critical mechanisms for adapting to changing environments and meeting of essential nutrient demand.

Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses

Possibly the last discovery of a previously unknown major ecosystem on Earth was made just over half a century ago, when researchers found teaming communities of animals flourishing two and a half kilometers below the ocean surface at hydrothermal vents. We now know that these highly productive ecosystems are based on nutritional symbioses between chemosynthetic bacteria and eukaryotes and that these chemosymbioses are ubiquitous in both deep-sea and shallow-water environments. The symbionts are primary producers that gain energy from the oxidation of reduced compounds, such as sulfide and methane, to fix carbon dioxide or methane into biomass to feed their hosts. This review outlines how the symbiotic partners have adapted to living together. We first focus on the phylogenetic and metabolic diversity of these symbioses and then highlight selected research directions that could advance our understanding of the processes that shaped the evolutionary and ecological success of these associations. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Microbial ecology of the dark ocean above, at, and below the seafloor

The majority of life on Earth--notably, microbial life--occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean-the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.-has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats.

Methanotrophic symbioses in marine invertebrates

Symbioses between marine animals and aerobic methane-oxidizing bacteria are found at hydrothermal vents and cold seeps in the deep sea where reduced, methane-rich fluids mix with the surrounding oxidized seawater. These habitats are 'oases' in the otherwise nutrient-poor deep sea, where entire ecosystems are fueled by microbial chemosynthesis. By associating with bacteria that gain energy from the oxidation of CH4 with O2 , the animal host is indirectly able to gain nutrition from methane, an energy source that is otherwise only available to methanotrophic microorganisms. The host, in turn, provides its symbionts with continuous access to both electron acceptors and donors that are only available at a narrow oxic - anoxic interface for free-living methanotrophs. Symbiotic methane oxidizers have resisted all attempts at cultivation, so that all evidence for these symbiotic associations comes from ultrastructural, enzymatic, physiological, stable isotope and molecular biological studies of the symbiotic host tissues. In this review, we present an overview of the habitats and invertebrate hosts in which symbiotic methane oxidizers have been found, and the methods used to investigate these symbioses, focusing on the symbioses of bathymodiolin mussels that have received the most attention among methanotrophic associations.

Macro-ecology of Gulf of Mexico cold seeps

Shortly after the discovery of chemosynthetic ecosystems at deep-sea hydrothermal vents, similar ecosystems were found at cold seeps in the Gulf of Mexico. Over the past two decades, these sites have become model systems for understanding the physiology of the symbiont-containing megafauna and the ecology of seep communities worldwide. Symbiont-containing bi-valves and siboglinid polychaetes dominate the communities, including five bathymodiolin mussel species and six vestimentiferan (siboglinid polychaete) species in the Gulf of Mexico. The mussels include the first described examples of methanotrophic symbiosis and dual methanotrophic/thiotrophic symbiosis. Studies with the vestimentiferans have demonstrated their potential for extreme longevity and their ability to use posterior structures for subsurface exchange of dissolved metabolites. Ecological investigations have demonstrated that the vestimentiferans function as ecosystem engineers and identified a community succession sequence from a specialized high-biomass endemic community to a low-biomass community of background fauna over the life of a hydrocarbon seep site.

Diversity, relative abundance and metabolic potential of bacterial endosymbionts in three Bathymodiolus mussel species from cold seeps in the Gulf of Mexico

Cold seeps in the Gulf of Mexico are often dominated by mussels of the genus Bathymodiolus that harbour symbiotic bacteria in their gills. In this study, we analysed symbiont diversity, abundance and metabolic potential in three mussel species from the northern Gulf of Mexico: Bathymodiolus heckerae from the West Florida Escarpment, Bathymodiolus brooksi from Atwater Valley and Alaminos Canyon, and 'Bathymodiolus' childressi, which co-occurs with B. brooksi in Alaminos Canyon. Comparative 16S rRNA sequence analysis confirmed a single methanotroph-related symbiont in 'B.' childressi and a dual symbiosis with a methanotroph- and thiotroph-related symbiont in B. brooksi. A previously unknown diversity of four co-occurring symbionts was discovered in B. heckerae: a methanotroph, two phylogenetically distinct thiotrophs and a methylotroph-related phylotype not previously described from any marine invertebrate symbiosis. A gene characteristic of methane-oxidzing bacteria, pmoA, was identified in all three mussel species confirming the methanotrophic potential of their symbionts. Stable isotope analyses of lipids and whole tissue also confirmed the importance of methanotrophy in the carbon nutrition of all of the mussels. Analyses of absolute and relative symbiont abundance in B. heckerae and B. brooksi using fluorescence in situ hybridization (FISH) and rRNA slot blot hybridization indicated a clear dominance of methanotrophic over thiotrophic symbionts in their gill tissues. A site-dependent variability in total symbiont abundance was observed in B. brooksi, with specimens from Alaminos Canyon harbouring much lower densities than those from Atwater Valley. This shows that symbiont abundance is not species-specific but can vary considerably between populations.

Symbioses of methanotrophs and deep-sea mussels (Mytilidae: Bathymodiolinae)

The symbioses between invertebrates and chemosynthetic bacteria allow both host and symbiont to colonize and thrive in otherwise inhospitable deep-sea habitats. Given the global distribution of the bathymodioline symbioses, this association is an excellent model for evaluating co-speciation and evolution of symbioses. Thus far, the methanotroph and chemoautotroph endosymbionts of mussels are tightly clustered within two independent clades of gamma Proteobacteria, respectively. Further physiological and genomic studies will elucidate the ecological and evolutionary roles that these bacterial clades play in the symbiosis and chemosynthetic community. Due to the overall abundance of the methanotrophic symbioses at hydrothermal vents and hydrocarbon seeps, they likely play a significant, but as of yet unquantified, role in the biogeochemical cycling of methane. With this in mind, the search for methanotrophic symbioses should not be restricted to these known deep-sea habitats, but rather should be expanded to include methane-rich coastal marine and freshwater environments inhabited by methanotrophs and bivalves. Our current understanding of the bathymodioline symbioses provides a strong foundation for future explorations into the origin, ecology, and evolution of methanotroph symbioses, which are now becoming possible through a combination of classical and advanced molecular techniques.

Identification of methanotrophic lipid biomarkers in cold-seep mussel gills: chemical and isotopic analysis

A lipid analysis of the tissues of a cold-seep mytilid mussel collected from the Louisiana slope of the Gulf of Mexico was used in conjunction with a compound-specific isotope analysis to demonstrate the presence of methanotrophic symbionts in the mussel gill tissue and to demonstrate the host's dependence on bacterially synthesized metabolic intermediates. The gill tissue contained large amounts of group-specific methanotrophic biomarkers, bacteriohopanoids, 4-methylsterols, lipopolysaccharide-associated hydroxy fatty acids, and type I-specific 16:1 fatty acid isomers with bond positions at delta 8, delta 10, and delta 11. Only small amounts of these compounds were detected in the mantle or other tissues of the host animal. A variety of cholesterol and 4-methylsterol isomers were identified as both free and steryl esters, and the sterol double bond positions suggested that the major bacterially derived gill sterol [11.0% 4 alpha-methyl-cholesta-8(14),24-dien-3 beta-ol] was converted to host cholesterol (64.2% of the gill sterol was cholest-5-en-3 beta-ol). The stable carbon isotope values for gill and mantle preparations were, respectively, -59.0 and -60.4% for total tissue, -60.6 and -62.4% for total lipids, -60.2 and-63.9% for phospholipid fatty acids, and -71.8 and 73.8% for sterols. These stable carbon isotope values revealed that the relative fractionation pattern was similar to the patterns obtained in pure culture experiments with methanotrophic bacteria (R.E. Summons, L.L. Jahnke, and Z. Roksandic, Geochim. Cosmochim. Acta 58: 2853-2863, 1994) further supporting the conversion of the bacteria methylsterol pool.

Assimilation of Inorganic Nitrogen by Marine Invertebrates and Their Chemoautotrophic and Methanotrophic Symbionts

Symbioses between marine invertebrates and their chemoautotrophic and methanotrophic symbionts are now known to exist in a variety of habitats where reduced chemical species are present. The utilization of chemical energy and reliance on C 1 compounds by these symbioses are well documented. Much less is known about their metabolism of nitrogen. Earlier work has shown that the tissues of organisms in these associations are depleted of 15 N compared with those of other marine organisms, indicating that local sources of nitrogen are assimilated and that novel mechanisms of nitrogen metabolism may be involved. Although these symbioses have access to rich sources of ammonium (NH 4 + and NH 3 ) and/or nitrate, several investigators have proposed that N 2 fixation may account for some of these isotope values. Here we report that [ 15 N]ammonium and, to a lesser degree, [ 15 N]nitrate are assimilated into organic compounds by Solemya reidi , a gutless clam containing S-oxidizing bacteria, and seep mussel Ia, an undescribed mytilid containing methanotrophic bacteria. In contrast, Riftia pachyptila , the giant hydrothermal vent tube worm symbiotic with S-oxidizing bacteria, assimilated nitrate but not exogenous ammonium. The rates of assimilation of these sources are sufficient to at least partially support C 1 compound metabolism. N 2 assimilation was not exhibited by the symbionts tested.

Independent phylogenetic origins of methanotrophic and chemoautotrophic bacterial endosymbioses in marine bivalves

The discovery of bacterium-bivalve symbioses capable of utilizing methane as a carbon and energy source indicates that the endosymbionts of hydrothermal vent and cold seep bivalves are not restricted to sulfur-oxidizing chemoautotrophic bacteria but also include methanotrophic bacteria. The phylogenetic origin of methanotrophic endosymbionts and their relationship to known symbiotic and free-living bacteria, however, have remained unexplored. In situ localization and phylogenetic analysis of a symbiont 16S rRNA gene cloned from the gills of a recently described deep-sea mussel species demonstrate that this symbiont represents a new taxon which is closely related to free-living, cultivable Type I methanotrophic bacteria. This symbiont is distinct from known chemoautotrophic symbionts. Thus, despite compelling similarities between the symbioses, chemoautotrophic and methanotrophic symbionts of marine bivalves have independent phylogenetic origins.

Evaluation of Methyl Fluoride and Dimethyl Ether as Inhibitors of Aerobic Methane Oxidation

Methyl fluoride (MF) and dimethyl ether (DME) were effective inhibitors of aerobic methanotrophy in a variety of soils. MF and DME blocked consumption of CH 4 as well as the oxidation of 14 CH 4 to 14 CO 2 , but neither MF nor DME affected the oxidation of [ 14 C]methanol or [ 14 C]formate to 14 CO 2 . Cooxidation of ethane and propane by methane-oxidizing soils was also inhibited by MF. Nitrification (ammonia oxidation) in soils was inhibited by both MF and DME. Production of N 2 O via nitrification was inhibited by MF; however, MF did not affect N 2 O production associated with denitrification. Methanogenesis was partially inhibited by MF but not by DME. Methane oxidation was ∼100-fold more sensitive to MF than was methanogenesis, indicating that an optimum concentration could be employed to selectively block methanotrophy. MF inhibited methane oxidation by cell suspensions of Methylococcus capsulatus ; however, DME was a much less effective inhibitor.

Chemosynthetic Mussels at a Brine-Filled Pockmark in the Northern Gulf of Mexico

A large (540 square meters) bed of Bathymodiolus n. sp. (Mytilidae: Bivalvia) rings a pool of hypersaline (121.35 practical salinity units) brine at a water depth of 650 meters on the continental slope south of Louisiana. The anoxic brine (dissolved oxygen </=0.17 milliliters per liter) contains high concentrations of methane, which nourishes methanotrophic symbionts in the mussels. The brine, which originates from a salt-cored diapir that penetrates to within 500 meters ofthe sea floor, fills a depression that was evidently excavated by escaping gas. The spatial continuity of the mussel bed indicates that the brine level has remained fairly constant; however, demographic differences between the inner and outer parts of the bed record small fluctuations.