Person: D'Arcy R. Meyer-Dombard

Abstract

Abstract

The availability of microbiological and geochemical data from island-based and high-arsenic hydrothermal systems is limited. Here, the microbial diversity in island-based hot springs on Ambitle Island (Papua New Guinea) was investigated using culture-dependent and -independent methods. Waramung and Kapkai are alkaline springs high in sulfide and arsenic, related hydrologically to previously described hydrothermal vents in nearby Tutum Bay. Enrichments were carried out at 24 conditions with varying temperature (45, 80 °C), pH (6.5, 8.5), terminal electron acceptors (O₂, SO₄ ²⁻, S⁰, NO₃ ⁻), and electron donors (organic carbon, H₂, As^III). Growth was observed in 20 of 72 tubes, with media targeting heterotrophic metabolisms the most successful. 16S ribosomal RNA gene surveys of environmental samples revealed representatives in 15 bacterial phyla and 8 archaeal orders. While the Kapkai 4 bacterial clone library is primarily made up of Thermodesulfobacteria (74 %), no bacterial taxon represents a majority in the Kapkai 3 and Waramung samples (40 % Proteobacteria and 39 % Aquificae, respectively). Deinococcus/Thermus and Thermotogae are observed in all samples. The Thermococcales dominate the archaeal clone libraries (65–85 %). Thermoproteales, Desulfurococcales, and uncultured Eury- and Crenarchaeota make up the remaining archaeal taxonomic diversity. The culturing and phylogenetic results are consistent with the geochemistry of the alkaline, saline, and sulfide-rich fluids. When compared to other alkaline, island-based, high-arsenic, or shallow-sea hydrothermal communities, the Ambitle Island archaeal communities are unique in geochemical conditions, and in taxonomic diversity, richness, and evenness.

Project Description

Data Project Maintainers

Abstract

In the Zambales ophiolite range, terrestrial serpentinizing fluid seeps host diverse microbial assemblages. The fluids fall within the profile of Ca²⁺-OH⁻-type waters, indicative of active serpentinization, and are low in dissolved inorganic carbon (DIC) (<0.5 ppm). Influx of atmospheric carbon dioxide (CO₂) affects the solubility of calcium carbonate as distance from the source increases, triggering the formation of meter-scale travertine terraces. Samples were collected at the source and along the outflow channel to determine subsurface microbial community response to surface exposure. DNA was extracted and submitted for high-throughput 16S rRNA gene sequencing on the Illumina MiSeq platform. Taxonomic assignment of the sequence data indicates that 8.1% of the total sequence reads at the source of the seep affiliate with the genus Methanobacterium. Other major classes detected at the source include anaerobic taxa such as Bacteroidetes (40.7% of total sequence reads) and Firmicutes (19.1% of total reads). Hydrogenophaga spp. increase in relative abundance as redox potential increases. At the carbonate terrace, 45% of sequence reads affiliate with Meiothermus spp. Taxonomic observations and geochemical data suggest that several putative metabolisms may be favorable, including hydrogen oxidation, H₂-associated sulfur cycling, methanogenesis, methanotrophy, nitrogen fixation, ammonia oxidation, denitrification, nitrate respiration, methylotrophy, carbon monoxide respiration, and ferrous iron oxidation, based on capabilities of nearest known neighbors. Scanning electron microscopy and energy dispersive X-ray spectroscopy suggest that microbial activity produces chemical and physical traces in the precipitated carbonates forming downstream of the seep’s source. These data provide context for future serpentinizing seep ecosystem studies, particularly with regards to tropical biomes.

Abstract

This study is the first to investigate the microbial ecology of the Tutum Bay (Papua New Guinea) shallow-sea hydrothermal system. The subsurface environment was sampled by SCUBA using push cores, which allowed collection of sediments and pore fluids. Geochemical analysis of sediments and fluids along a transect emanating from a discrete venting environment, about 10 mbsl, revealed a complex fluid flow regime and mixing of hydrothermal fluid with seawater within the sediments, providing a continuously fluctuating redox gradient. Vent fluids are highly elevated in arsenic, up to ∼1 ppm, serving as a “point source” of arsenic to this marine environment. 16S rRNA gene and FISH (fluorescence in situ hybridization) analyses revealed distinct prokaryotic communities in different sediment horizons, numerically dominated by Bacteria. 16S rRNA gene diversity at the genus level is greater among the Bacteria than the Archaea. The majority of taxa were similar to uncultured Crenarchaea, Chloroflexus, and various heterotrophic Bacteria. The archaeal community did not appear to increase significantly in number or diversity with depth in these sediments. Further, the majority of sequences identifying with thermophilic bacteria were found in the shallower section of the sediment core. No 16S rRNA genes of marine Crenarchaeota or Euryarchaeota were identified, and none of the identified Crenarchaeota have been cultured. Both sediment horizons also hosted “Korarchaeota”, which represent 2–5% of the 16S rRNA gene clone libraries. Metabolic functions, especially among the Archaea, were difficult to constrain given the distant relationships of most of the community members from cultured representatives. Identification of phenotypes and key ecological processes will depend on future culturing, identification of arsenic cycling genes, and RNA-based analyses.

Abstract

The shallow submarine hydrothermal systems of Tutum Bay, Papua New Guinea, are an ideal opportunity to study the influence of arsenic on a marine ecosystem. Previous reports have demonstrated that the hydrothermal vents in Tutum Bay release arsenic in reduced hydrothermal fluids into the marine environment at the rate of 1.5 kg of arsenic/day. Aqueous arsenite is oxidized and adsorbed onto hydrous ferric oxides [HFOs] surrounding the venting area. We demonstrate here that microorganisms are key in both the oxidation of Fe^II and As^III in the areas immediately surrounding the vent source. Surveys of community diversity in biofilms and in vent fluid indicate the presence of zeta-Proteobacteria, alpha-Proteobacteria, Persephonella, and close relatives of the archaeon Nitrosocaldus. The iron oxidizing zeta-Proteobacteria are among the first colonizers of solid substrates near the vents, where they appear to be involved in the precipitation of the hydrous ferric oxides (HFOs). Further, the biofilm communities possess the genetic capacity for the oxidation of arsenite. The resulting arsenate is adsorbed onto the HFOs, potentially removing the arsenic from the immediate marine system. No evidence was found for dissimilatory arsenate reduction, but the arsenate may be remobilized by detoxification mechanisms. This is the first demonstration of the genetic capacity for arsenic cycling in high temperature, shallow-sea vent communities, supporting recent culture-based findings in similar systems in Greece (Handley et al., 2010). These reports extend the deep-sea habitat of the zeta-Proteobacteria to shallow submarine hydrothermal systems, and together implicate biological oxidation of both iron and arsenite as primary biogeochemical processes in these systems, providing a mechanism for the partial removal of aqueous arsenic from the marine environment surrounding the vents.

Abstract

This study assessed deep subsurface-to-surface transitional microbial communities in two serpentinizing ecosystems: a flaming gas/fluid seep in Yanartaş, Turkey and a bubbling fluid seep in Manleluag Spring National Park, the Philippines. These systems exhibited some similar geochemical and taxonomic attributes, but different physical properties that help demonstrate the effect surface conditions have on the subsurface. 16S rRNA gene sequencing, coupled with metagenomic and geochemical analysis, reveal dynamic microbial ecosystems supported partly by the products of active serpentinization. At Yanartaş, the fluid seeps may be ephemeral. Large travertine deposits are visible on the mountain slope as relicts of former fluid seeps. At Manleluag, the tropical climate causes monsoon and “dry” seasons, which influence dissolved inorganic and organic carbon input in the system. The 16S rRNA gene sequencing and metagenomic shotgun sequencing data suggest that, despite differences in regional climate and vegetation cover, Manleluag and Yanartaş exhibit taxonomic and functional similarities. Metabolisms involving methane, nitrogen, iron, and sulfur cycling, hydrogen oxidation, and respiration were detected in both 16S rRNA amplicon and metagenomic sequence datasets. Metagenomic analysis detected genes involved with osmotic and oxidative stress at both sites, and sporulation and dormancy genes at Manleluag. Several transposable elements were also reported at both Manleluag and Yanartaş. These mechanisms may allow subsurface microbial communities to adapt to surface conditions. In general, the surface and subsurface environment appear to be inherently connected at Yanartaş and Manleluag; the surface and subsurface both shape the microbial community in these ecosystems, and the microbial community alters the biogeochemistry.

Abstract

The subseafloor biosphere associated with deep-sea hydrothermal vents sustains a diverse range of chemical energy sources capable of driving chemolithoautotrophic metabolism. Based upon studies of microbial isolates, there are at least six known pathways of carbon fixation, each with a unique phylogenetic distribution, and specific requirements for energy, metal cofactors, and reducing power. All of the newest pathways have been elucidated in thermophilic and hyperthermophilic microorganisms, particularly Archaea. As these studies require the enrichment and isolation of pure cultures, which can be challenging even in temperate environments, the overall diversity of carbon fixation pathways, how, and why they vary under different environmental conditions is unknown. We propose that studying microbial carbon fixation in anaerobic, thermophilic microcosm experiments by tracing 13-C labeled DIC into DNA and subsequently sequencing its meta-genome, will elucidate both who is fixing carbon at high temperatures and how it is being fixed. This work will complement phylogenomic and biogeochemical studies associated with CORK observatories installed on the eastern flank of the Juan de Fuca Ridge. Results of this work will provide critical data to integrate with rate measurements of biogeochemical activities and with cultivation independent genomic data derived from the subseafloor biosphere.