Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys

Abstract

The Lost City Hydrothermal Field, an ultramafic-hosted system located 15 km west of the Mid-Atlantic Ridge, has experienced at least 30,000 years of hydrothermal activity. Previous studies have shown that its carbonate chimneys form by mixing of approximately 90 degrees C, pH 9-11 hydrothermal fluids and cold seawater. Flow of methane and hydrogen-rich hydrothermal fluids in the porous interior chimney walls supports archaeal biofilm communities dominated by a single phylotype of Methanosarcinales. In this study, we have extensively sampled the carbonate-hosted archaeal and bacterial communities by obtaining sequences of >200,000 amplicons of the 16S rRNA V6 region and correlated the results with isotopic ((230)Th) ages of the chimneys over a 1,200-year period. Rare sequences in young chimneys were commonly more abundant in older chimneys, indicating that members of the rare biosphere can become dominant members of the ecosystem when environmental conditions change. These results suggest that a long history of selection over many cycles of chimney growth has resulted in numerous closely related species at Lost City, each of which is preadapted to a particular set of reoccurring environmental conditions. Because of the unique characteristics of the Lost City Hydrothermal Field, these data offer an unprecedented opportunity to study the dynamics of a microbial ecosystem's rare biosphere over a thousand-year time scale.

Fig. 1.

Location within the Lost City Hydrothermal Field of carbonate chimney samples from which sequences were collected. Sample 1 was obtained from the pinnacle of the main edifice known as Poseidon, 50 m above the flange from which samples 2 and 3 were collected. Sample 4 is from a small, isolated chimney with no apparent venting activity found near the bottom of a cliff face. Scale bars in all photographs are 10 cm.

Fig. 2.

Rarefaction analysis of archaeal and bacterial V6 tag sequences for each of the four chimney samples. OTUs, operational taxonomic units defined by clustering sequences with a 3% pairwise distance threshold. Bacterial diversity (curves outlined in black) is clearly greater than archaeal diversity in all samples. Rarefaction curves for archaeal sequences are near-asymptotic, indicating nearly complete sampling of archaeal V6 amplicon libraries. Dashed line indicates the point to which data were subsampled to compare diversity values among samples in Table 1.

Fig. 3.

Relative abundance distribution of archaeal OTUs among samples. (A) Bootstrapped phylogenetic tree of full-length archaeal 16S rRNA clones showing the relationship of three Lost City clones (in bold) to previously published close relatives. (B) Relative normalized abundance (as percentage of total tag sequences per sample) of each archaeal OTU (clustered at 3% distance threshold) in each of the four chimney samples. The OTUs are labeled according to which of the three groups they belong according to pairwise similarity with the V6 region of the full-length 16S rRNA clones. ANME-1, anaerobic methanotrophic archaea; LCMS, Lost City Methanosarcinales; MGI, Marine Group I Crenarchaeota.

Fig. 4.

Relative abundance distribution of bacterial OTUs among samples. OTUs are labeled according to their taxonomic assignment by the GAST process (22). α, Alphaproteobacteria; Bact, Bacteroides; Cflx, Chloroflexus; δ, Deltaproteobacteria; ε, Epsilonproteobacteria; Firm, Firmicutes; γ, Gammaproteobacteria.

Fig. 5.

Relative abundance distribution of Thiomicrospira-related OTUs among samples. (A) Bootstrapped phylogenetic tree of full-length 16S rRNA clones showing the relationship of Lost City clones (in bold) to previously published Thiomicrospira clones. (B) Relative normalized abundance of each OTU assigned to genus Thiomicrospira by GAST (22) in each of the four chimney samples. Pairwise similarities between sequences representative of each OTU and the V6 region of each clone were calculated, and OTUs were grouped according to which clone they were most closely related, as indicated by A–E labels. In groups A–D, similarities between sequences and clones ranged from 93 to 100%; in group E, 86–100%. OTUs within each group that have the highest similarity to the clone are sorted to the left.