Edited by: Jesse G. Dillon, California State University, Long Beach, United States
Reviewed by: Karthik Anantharaman, University of California, Berkeley, United States; Craig Lee Moyer, Western Washington University, United States
*Correspondence: Xiang Xiao
This article was submitted to Extreme Microbiology, a section of the journal Frontiers in Microbiology
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Southwest Indian Ridge (SWIR) is a typical oceanic ultraslow spreading ridge with intensive hydrothermal activities. The microbial communities in hydrothermal fields including primary producers to support the entire ecosystem by utilizing geochemical energy generated from rock-seawater interactions. Here we have examined the microbial community structures on four hydrothermal vents from SWIR, representing distinct characteristics in terms of temperature, pH and metal compositions, by using Illumina sequencing of the 16S small subunit ribosomal RNA (rRNA) genes, to correlate bacterial and archaeal populations with the nature of the vents influenced by ultraslow spreading features.
Hydrothermal venting is one of the fundamental processes by which heat and chemical species are transferred from the lithosphere to the ocean, and venting occurs along divergent plate boundaries in every ocean, at all spreading rates, and in a diversity of geological settings (Baker and German,
Deep-sea hydrothermal vents are some of the most biologically productive ecosystems on the Earth, yet receive little to no input of organic matter derived photosynthetically (Rutherford,
Low- and high-temperature chimney samples were collected during November 2014-January 2015 Dayang 35 cruise to the Longqi field by using the manned submersible
Schematic location of the sampling sites and Longqi vent Field (red Pentagram) at SWIR. The map was created using python.
Concentrations of Elements in chimney deposits and physicochemical characteristics of their hydrothermal fluids at the Longqi field on SWIR.
Fe | 261,600 | 305,900 | 286,500 | 68,780 | |
S | 300,200 | 394,400 | 302,400 | 1,682 | |
Zn | 211,200 | 233,100 | 2,938 | 154 | |
Mn | 3,786 | 33 | 14 | 343,800 | |
Mg | 20,960 | 24 | 324 | 13,720 | |
Ca | 9,268 | 112 | 46,000 | 13,140 | |
Pb | 1,417 | 703 | 57 | 41 | |
Cu | 806.8 | 541 | 67,330 | 42 | |
Al | 661.6 | 5,680 | 141 | 429 | |
Depth (m) | 2,746 | 2,768 | 2,778 | 2,775 | |
Location | 49.6501525°E, 37.7832506°S | 49.6487677°E, 37.7832151°S | 49.6487677°E, 37.7832151°S | 49.6477092°E, 37.7799720°S | |
Max. Temp. (°C) | 145 | 13.3 | 362 | 379 | 13.3–379 |
pH | 4.85 | – | – | 3.42 | 3.21–4.85 |
Salinity | 4.0 | – | – | 4.0 | 3.7–4.5 |
DO (mg L−1) | 24.7 | – | – | 14.3 | 0.5–24.7 |
For chimney samples, named as JL90, JL94D, JL94H, and JL95 from SWIR, and CH7 from EPR9°N (Figure
Data analysis of the 16S rRNA Miseq sequence was performed using QIIME version 1.9.1 software pipeline (Caporaso et al.,
Mineral analysis of the chimney samples was obtained using X-Ray Fluorescence Spectrometer (XRF-1800, Shimadzu Japan), X-Ray Polycrystaline Diffractometer (D8 Advance, Bruker, German) and ICP-AES (iCAP6300, Thermo, USA). Powder XRF and XRD samples were dried overnight at 70°C and deposited on sample holders. The procedure for XRF and XRD analysis was carried out according to the methods described in details by Peng et al. (
The temperature of fluids at sampling vent sites ranged from a low temperature of 13.3°C for JL90 to a high-temperature reached 379°C at JL95. The pH of the venting fluid, the salinity and DO of surrounding deep-sea water are given in Table
We targeted the V4-V5 region to characterize the archaeal communities, and V4 region for bacterial communities associated with hydrothermal deposits according to previous report (Flores et al.,
Diversity estimates from 16S rRNA amplicon libraries: miseq tag sequences.
JL90A |
HT-Active sulfide | 665 | 16,548 | 4.61 (±0.02) |
JL94DA | LT-Active sulfide | 1,497 | 38,787 | 5.67 (±0.04) |
JL94HA | HT-Active sulfide | 774 | 51,649 | 4.54 (±0.03) |
JL95A | HT-Active sulfide | 2,034 | 49,777 | 6.79 (±0.04) |
CH7A | LT-Active sulfide | 794 | 24,720 | 4.14 (±0.01) |
JL90B |
HT-Active sulfide | 1,563 | 50,336 | 6.52 (±0.04) |
JL94DB | LT-Active sulfide | 1,305 | 19,932 | 7.53 (±0.02) |
JL94HB | HT-Active sulfide | 1,085 | 22,691 | 6.76 (±0.03) |
JL95B | HT-Active sulfide | 4,336 | 12,203 | 10.50 (±0.01) |
CH7B | LT-Active sulfide | 1,034 | 29,856 | 5.85 (±0.02) |
Based on the alpha-diversity of each chimney and the beta-diversity among target chimney samples in this study, we attempted to evaluate how the microbial community differences link to possible biogeographic functions.
Overall, the four chimney samples from SWIR contained 12 phyla of archaea. The shared communities at different chimney samples were further evaluated. It was found that 11 were shared and only one of the 12 phyla, the candidate phylum SM1K20 was absent in JL90. Over 24% relative abundance of the
Taxonomic relative abundance of archaeal classes observed of chimney samples for Longqi vent field at SWIR. Bar charts show the Kingdom; Phylum distribution for taxonomically assigned tags that occurred more than 1,000 times.
Taxonomic relative abundance of
The four sulfide samples contained 29 similar phyla except the absence of
Taxonomic breakdown of bacterial 16S rRNA V4-region tags from each chimney sample. Pie Charts show Phylum; Class; Order distribution (The average relative abundance among samples is over 1%) for taxomomically assigned tags that occurred more than 1,000 times; the remaining tag sequences are grouped into “Other.”
Relative abundance of Gammaproteobacteria taxa observed in each chimney sample for Longqi field at SWIR. “others” represents the less abundant genera of Acinetobacter, Sedimenticola, Marinicella, Colwellia, Arenicellaceae, Marine methylotrophic Group 2, Coxiella, Granulosicoccus, and unclassified Gammaproteobacteria. Groups which were detected below1% are indicated with a blue oplus, between 1 and 2% are indicated with a blue diamond.
Relative abundance of Epsilonproteobacteria genera observed in each chimney samplefor Longqi field at SWIR. Groups which were detected below1% are indicated with a blue oplus, between 1 and 2% are indicated with a diamond.
In this study, high-throughput, DNA-based analysis of environmental samples has been applied to investigate the microbial communities of chimney samples collected from Longqi hydrothermal field. Recent studies have found archaeal DNA was poorly recovered from lower temperature, diffuse flow vents or inactive chimneys (Bourbonnais et al.,
According to the Venn diagrams showing (Figure
Microbial community structures were clearly correlated to the environmental parameters, and among all the considered parameters the
Potential energy sources for deep-sea vent chemoautotrophy include reduced sulfur compounds, molecular hydrogen, reduced metals and ammonium. Classic sulfur-oxidizing bacteria have been detected as the dominant families, suggesting a strong sulfur-metabolizing potential in all tested chimney samples (Table
Potential ecological function of tag sequences for which obvious metabolisms can be inferred.
S oxidation | 0.016 | 0.105 | 1.780 | 0.000 | |
36.326 | 24.724 | 8.633 | 1.246 | ||
0.193 | 0.040 | 0.855 | 1.065 | ||
5.360 | 5.955 | 4.160 | 1.950 | ||
2.908 | 0.642 | 0.282 | 0.295 | ||
0.971 | 0.191 | 2.728 | 2.663 | ||
Sulfate reduction | 0.429 | 0.657 | 22.053 | 0.246 | |
0.006 | 0.557 | 0.154 | 0.008 | ||
0.034 | 1.786 | 0.604 | 0.016 | ||
3.028 | 5.398 | 3.790 | 0.131 | ||
0.360 | 0.627 | 0.194 | 0.008 | ||
0.022 | 0.060 | 1.044 | 0.008 | ||
49.653 | 40.742 | 46.277 | 7.636 | ||
Ammonia oxidation | 1.196 | 0.115 | 0.375 | 1.868 | |
Nitrite oxidation | 0.002 | 0.005 | 0.026 | 0.992 | |
Nitrate reduction | 0.489 | 0.105 | 0.062 | 0.057 | |
Nitrification | 0.002 | 0.010 | 0.004 | 1.418 | |
N fixation | 5.739 | 0.562 | 0.450 | 2.622 | |
7.428 | 0.797 | 0.917 | 6.957 | ||
H oxidation | 0.028 | 0.080 | 1.908 | 0.016 | |
0.072 | 0.261 | 4.958 | 0.033 | ||
0.290 | 0.025 | 0.198 | 0.008 | ||
0.39 | 0.366 | 7.064 | 0.057 | ||
CH4 oxidation | 1.122 | 0.161 | 2.318 | 0.057 | |
Fe(II) oxidation | 1.295 | 2.468 | 1.084 | 0.705 | |
Fe(III) reduction | 0.238 | 1.801 | 0.591 | 0.041 | |
2.655 | 4.43 | 3.993 | 0.803 | ||
Mn oxidation | 0.068 | 1.234 | 0.353 | 0.049 | |
Total bacteria | 60.194 | 47.569 | 58.604 | 15.502 | |
Sulfate reduction | 0.538 | 0.003 | 7.460 | 0.014 | |
0.326 | 0.003 | 1.111 | 0.004 | ||
Ammonia oxidation | 45.667 | 1.062 | 24.636 | 42.745 | |
Total archaea | 46.531 | 1.068 | 33.207 | 42.763 |
Ammonia oxidation is the first step of nitrification, in which ammonia is first oxidized to nitrite by ammonia-oxidizing bacteria and/or archaea (AOB or AOA), then subsequently to nitrate by nitrite-oxidizing bacteria (NOB). The
The reduced metals (Fe, Mn, Cu, etc.,) are the endmembers in vent fluids and potential energy sources for deep-sea vent chemoautotrophs. Fe(II) is a common and often the most dominant metal. Microaerophilic Fe-oxidizing microorganisms (FeOM) colonize gradients of Fe(II) and oxygen, taking advantage of the available chemical energy. Vast communities of FeOM proliferate at deep sea hydrothermal vents, forming mineralized mats (Chan et al.,
Hydrogen has also been shown to be an important energy source in vent fluids at the Logatchev and Rainbow fields on the Mid-Atlantic Ridge (Takai et al.,
To evaluate the effects of geological and geochemical characteristic on microbial communities on the surface of active chimneys in Longqi field at SWIR, we compared the bacterial and archaeal distribution pattern with habitats of active chimney both from slow-spreading ridge of MAR and fast-spreading ridge of EPR. Overall, the microbial composition on active chimneys recovered by tag sequencing at SWIR in our libraries was different from hydrothermal vents at EPR and MAR by using cluster analysis (Figures
Clustering analysis tree of the archaeal community structure of chimneys from SWIR, EPR and MAR. LS7 = Lucky Strike. Lucky Strike vent field located at MAR (Flores et al.,
Clustering analysis tree of the bacterial community structure of chimneys from SWIR, EPR and MAR. LS7 = Lucky Strike. Lucky Strike vent field located at MAR (Flores et al.,
This study reported the distribution and diversity of the prokaryotic communities on the surface of chimneys collected from Longqi field the SWIR. The 16S rRNA gene analysis suggested that bacterial communities were highly diversified among all the detected samples. Compared to bacteria, the lower diversity of archaeal phylotypes agreed with other molecular surveys indicating that marine hydrothermal vent archaeal diversity is relatively limited (Huber et al.,
HJ and YZ: did the sampling during cruise; XX and JD: designed experiments; JD and HW: carried out experiments; JD, HW, and HL: analyzed experimental results; HL: assisted with Illumina sequencing. JD and YZ: wrote the manuscript.
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
This work was supported by China Ocean Mineral Resources R&D Association (Grant No. DY125-22-04), and National Natural Science Foundation of China (Grant No. 41530967). We would like to thank the crew and scientific team of R/V Xiangyanghong09, the pilots and the supporting team of Jiaolong manned submersible in 35th Dayang Cruise, the crew and scientific team of R/V Atlantis in cruise AT26-10, for the sampling. We also thank Jiahua Wang and Xiaoyuan Feng for the help to analyse the 16S rRNA Miseq sequencing data.
The Supplementary Material for this article can be found online at: