Diversity and Metabolic Potentials of Subsurface Crustal Microorganisms from the Western Flank of the Mid-Atlantic Ridge

Abstract

Deep-sea oceanic crust constitutes the largest region of the earth’s surface. Accumulating evidence suggests that unique microbial communities are supported by iron cycling processes, particularly in the young (<10 million-year old), cool (<25°C) subsurface oceanic crust. To test this hypothesis, we investigated the microbial abundance, diversity, and metabolic potentials in the sediment-buried crust from “North Pond” on western flank of the Mid-Atlantic Ridge. Three lithologic units along basement Hole U1383C were found, which typically hosted ∼104 cells cm-3 of basaltic rock, with higher cell densities occurring between 115 and 145 m below seafloor. Similar bacterial community structures, which are dominated by Gammaproteobacterial and Sphingobacterial species closely related to iron oxidizers, were detected regardless of variations in sampling depth. The metabolic potentials of the crust microbiota were assayed by metagenomic analysis of two basalt enrichments which showed similar bacterial structure with the original sample. Genes coding for energy metabolism involved in hydrocarbon degradation, dissimilatory nitrate reduction to ammonium, denitrification and hydrogen oxidation were identified. Compared with other marine environments, the metagenomes from the basalt-hosted environments were enriched in pathways for Fe3+ uptake, siderophore synthesis and uptake, and Fe transport, suggesting that iron metabolism is an important energy production and conservation mechanism in this system. Overall, we provide evidence that the North Pond crustal biosphere is dominated by unique bacterial groups with the potential for iron-related biogeochemical cycles.

Hemolymph Microbiomes of Three Aquatic Invertebrates as Revealed by a New Cell Extraction Method

“…An average of 200 fields of view were counted for each membrane. The area of each field of view was set at 10,000 m 2 , and the detection limit was ϳ10 3 cells/ml for a 95% probability of detecting at least 1 cell, as described previously (21,22). The blank control was performed with autoclaved and 0.2-m-pore-size mesh membrane-filtered Milli-Q water (18.2 M⍀; Millipore, USA) and processed with the same filtration and staining steps as the bacterial samples.…”

“…Equimolar concentrations of each purified PCR product were pooled and sequenced on an Illumina HiSeq 2500 platform (2 ϫ 250 bp; Illumina, USA), according to standard protocols. Processing of raw sequence data was performed as described elsewhere (21). Briefly, raw reads which contained a 50-bp continuous fragment with an average quality score less than 30 and/or any ambiguities were removed.…”

“…are absent in the microbial community (14). In this regard, culture-independent strategies (including enumeration of microbial cells by fluorescence microscopy and characterization of microbial community structures and metabolic functions by high-throughput sequencing of the 16S rRNA genes as well as metagenomics [21,22]) are promising alternatives. Unfortunately, one major problem that hinders the application of culture-independent methods is the extremely low abundance of microbial cells in hemolymph (Ͻ10 4 CFU/ml; Table 1) compared to that of hemocytes (Ͼ10 6 hemocytes/ml) (see Fig.…”

Indigenous Ammonia-Oxidizing Archaea in Oxic Subseafloor Oceanic Crust

“…Previous studies at this site have revealed diverse microbial communities with abundances of up to ϳ10 5 cells g Ϫ1 rock in the igneous crust (15,19,24). In addition, microbial nitrogen transformation occurs in the overlying sediments from the sediment-water interface down to the basement, resulting in a downward flux of nitrate into the underlying oceanic crust (25).…”

“…Despite the potentially global importance of microbial life within the upper crust, fundamental questions regarding cellular recruitment, extent of activity, niche partitioning, and community succession in this habitat remain unanswered. There have been only a few published studies dedicated to microbial interrogation of native subseafloor crustal rocks (1,(14)(15)(16)(17) and even fewer that have addressed the potential biogeochemical functions of these communities (16,18). Based on the limited body of literature, it appears that microbial communities in the subseafloor crust are unique in comparison to those found in hydrothermal plumes, deep seawater, and hydrothermal fluids and in seafloor exposed basalt (12) and the overlying sediments (19).…”