Bacterial Number and Genetic Diversity in a Permafrost Peatland (Western Siberia): Testing a Link with Organic Matter Quality and Elementary Composition of a Peat Soil Profile
Abstract
:1. Introduction
2. Study Site and Methods
2.1. Peat Core Collection and Temperature Pattern of the WSL Peat Profile
2.2. Total Chemical Analysis
2.3. Organic Matter Isotopic Composition and Quality
2.4. Analysis of Bacterial Number and Genetic Diversity
2.5. Statistical Treatment
3. Results
3.1. Peat Formation History, Thermal Regime, Physical and Elementary Characteristics of the Peat Core and Chemical Composition of the Pore Water
3.2. Organic Matter Isotopic Composition and Functional Group Analysis by NMR
3.3. Cell Number and Microbial Diversity as a Function of Depth
3.4. Pair Correlation and Multiparametric Statistics of the Full Data Set
4. Discussion
4.1. Elementary Peat and Peat Fluid Composition and Organic Matter Quality
4.2. Bacterial Number and Genetic Diversity of Soil Microorganisms
4.3. Multiple Factors Governing the Microbial Diversity in the Peat Core
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Depth, cm | Substrate | Average Depth, cm | Average T, °C | Minimal T, °C | Maximal T, °C | Peat, Bulk Density, g/cm3 | Degree of Decomposition, % |
---|---|---|---|---|---|---|---|
10–20 | peat | −15 | −0.047 | −8.4 | 11.3 | 0.16 | 5 |
30–40 | peat | −35 | −0.63 | −6.1 | 4.4 | 0.29 | 10 |
50–60 | peat | −55 | −0.8 | −4.1 | 0.2 | 0.29 | 17 |
70–80 | peat | −75 | −0.74 | −2.8 | −0.1 | 0.23 | 30 |
90–100 | peat | −95 | −0.65 | −2.3 | −0.1 | 0.23 | 32 |
100–110 | mineral | −105 | −0.58 | −1.3 | −0.1 | 1.30 | |
Depth, cm | substrate | N, % | C, % | C:N | L* by CIE lab | a* by CIE lab | b* by CIE lab |
10–20 | peat | 0.79 | 44.6 | 56.1 | 43.7 | 9.9 | 16.5 |
30–40 | peat | 0.61 | 46.0 | 75.4 | 39.2 | 9.1 | 17.5 |
50–60 | peat | 0.83 | 40.6 | 48.9 | 33.2 | 8.7 | 17.5 |
Depth, cm | substrate | N, % | C, % | C:N | L* by CIE lab | a* by CIE lab | b* by CIE lab |
70–80 | peat | 1.36 | 56.1 | 41.3 | 25.9 | 7.8 | 14.0 |
90–100 | peat | 0.84 | 54.41 | 64.8 | 25.3 | 6.9 | 12.3 |
100–110 | mineral | 0.03 | 1.905 | 63.5 | 66.2 | 3.9 | 10.6 |
Depth, cm | substrate | S, % | P-lab, mg/kg | δ13C | δ15N | Alkyl C | O-alkyl C |
10–20 | peat | 0.38 | 0.76 | −24.7 | 4.4 | 24.05 | 71.9 |
30–40 | peat | 0.38 | 0.34 | −25.9 | 4.8 | 15.3 | 77.3 |
50–60 | peat | 0.29 | 0.06 | −26.4 | 4.25 | 26.2 | 63.9 |
70–80 | peat | 0.39 | 0.04 | −26.9 | 3.7 | 37.1 | 50.5 |
90–100 | peat | 0.22 | 0.03 | −26.2 | 4.1 | 47.1 | 39.3 |
100–110 | mineral | 0.05 | 0.00 | −26.9 | |||
Depth, cm | substrate | aromatic C | carboxylic C | Li peat | B peat | Na peat | Mg peat |
ppb | |||||||
10–20 | peat | 1.6 | 2.3 | 577 | 4518 | 372,422 | 296,970 |
30–40 | peat | 5.2 | 2.2 | 294 | 4544 | 103,287 | 327,233 |
50–60 | peat | 7.8 | 2.1 | 498 | 4434 | 72,538 | 194,873 |
70–80 | peat | 10.4 | 2.0 | 294 | 4892 | 29,929 | 169,643 |
90–100 | peat | 10.1 | 3.5 | 424 | 11,608 | 83,755 | 145,879 |
100–110 | mineral | 2441 | 3359 | 235,580 | 74,206 | ||
Depth, cm | substrate | Al peat | P peat | K peat | Ca peat | Ti peat | V peat |
ppb | |||||||
10–20 | peat | 2,302,515 | 448,947 | 938,435 | 1,049,413 | 183,028 | 3059 |
30–40 | peat | 1,392,605 | 295,471 | 232,556 | 1,525,343 | 52,626 | 1199 |
50–60 | peat | 1,813,247 | 209,406 | 284,074 | 911,927 | 86,250 | 1987 |
70–80 | peat | 1,925,618 | 200,513 | 192,876 | 921,297 | 59,999 | 1936 |
90–100 | peat | 2,797,844 | 172,804 | 327,006 | 832,506 | 116,491 | 2942 |
100–110 | mineral | 1,748,772 | 22,357 | 991,020 | 279,474 | 218,869 | 1677 |
Depth, cm | substrate | Cr peat | Mn peat | Fe peat | Co peat | Ni peat | Cu peat |
ppb | |||||||
10–20 | peat | 2504 | 10,234 | 1,311,464 | 281 | 1169 | 2138 |
30–40 | peat | 1966 | 5228 | 1,433,817 | 426 | 1083 | 594 |
50–60 | peat | 2745 | 5699 | 472,019 | 218 | 942 | 1152 |
70–80 | peat | 2793 | 2139 | 451,913 | 284 | 1841 | 2718 |
90–100 | peat | 3871 | 5225 | 519,426 | 522 | 1573 | 5064 |
100–110 | mineral | 1895 | 8516 | 290,073 | 177 | 263 | 914 |
Depth, cm | substrate | Zn peat | As peat | Rb peat | Sr peat | Y peat | Zr peat |
ppb | |||||||
10–20 | peat | 15,946 | 1354 | 3086 | 9573 | 618 | 3614 |
30–40 | peat | 15,957 | 315 | 748 | 13,479 | 345 | 1356 |
Depth, cm | substrate | Zn peat | As peat | Rb peat | Sr peat | Y peat | Zr peat |
ppb | |||||||
50–60 | peat | 7367 | 261 | 1185 | 8224 | 463 | 2777 |
70–80 | peat | 9325 | 391 | 694. | 8406 | 332 | 1843 |
90–100 | peat | 17,238 | 380 | 1084 | 8394 | 414 | 5941 |
100–110 | mineral | 2355 | 299 | 2854 | 7518 | 913 | 14,104 |
Depth, cm | substrate | Nb peat | Mo peat | Cd peat | Sb peat | Cs peat | Ba peat |
ppb | |||||||
10–20 | peat | 476 | 155 | 130 | 260 | 189 | 27,243 |
30–40 | peat | 462 | 87 | 132 | 39 | 46 | 20,066 |
50–60 | peat | 863 | 88 | 71 | 29 | 72 | 22,801 |
70–80 | peat | 579 | 211 | 86 | 42 | 41 | 29,938 |
90–100 | peat | 887 | 108 | 72 | 37 | 65 | 39,452 |
100–110 | mineral | 924 | 48 | 14 | 139 | 83 | 69,278 |
Depth, cm | substrate | La peat | Ce peat | Dy peat | Yb peat | Pb peat | U peat |
ppb | |||||||
10–20 | peat | 1184 | 2365 | 120 | 69 | 6485 | 80 |
30–40 | peat | 537 | 1167 | 72 | 32 | 1009 | 50 |
50–60 | peat | 775 | 1559 | 90 | 54 | 647 | 92 |
70–80 | peat | 534 | 1090 | 65 | 35 | 532 | 88 |
90–100 | peat | 727 | 1413 | 83 | 47 | 837 | 111 |
100–110 | mineral | 850 | 1498 | 108 | 86 | 1036 | 162 |
Depth, cm | substrate | Humidity, % | |||||
10–20 | peat | 317 | |||||
30–40 | peat | 337 | |||||
50–60 | peat | 700 | |||||
70–80 | peat | 458 | |||||
90–100 | peat | 650 | |||||
100–110 | mineral | 82 |
Depth | δ13C | δ15N | Alkyl C | O-Alkyl C | Aromatic C | Carbonyl C | Alkyl C: O-Alkyl C |
---|---|---|---|---|---|---|---|
‰ | ‰ | % | |||||
(0–5) | −23.6 | 2.8 | 16.7 | 79.8 | 0.0 | 3.5 | 0.21 |
(19–21) | −25.8 | 6.0 | 31.4 | 64.1 | 3.3 | 1.2 | 0.49 |
(30–35) | −25.9 | 4.8 | 15.3 | 77.3 | 5.2 | 2.2 | 0.20 |
(65–75) | −26.7 | 3.3 | 30.5 | 57.5 | 10.4 | 1.7 | 0.53 |
(75–85) | −27.1 | 4.1 | 43.7 | 43.5 | 10.4 | 2.4 | 1.00 |
(85–95) | −26.2 | 4.1 | 47.1 | 39.3 | 10.1 | 3.5 | 1.20 |
(105–115) | −26.9 | n.m * | n.m * | n.m * | n.m * | n.m * | n.m * |
Abbreviation | Taxon Unit (Phylum: Class) | Peat Horizon Depth, cm | |||||
---|---|---|---|---|---|---|---|
10–20 | 30–40 | 50–60 | 70–80 | 90–100 | 100–110 | ||
Share of 16S rRNA Gene Sequences in % of the Number of Obtained Sequences | |||||||
EuMeth | Euryarchaeota; Methanobacteria | 0.0 | 0.1 | 0.0 | 0.0 | 0.3 | 0.0 |
ThNit | Thaumarchaeota; Nitrososphaeria | 0.0 | 0.0 | 0.0 | 0.0 | 0.5 | 0.1 |
Ac | Acidobacteria; Acidobacteriia | 20.5 | 46.0 | 64.7 | 44.8 | 1.0 | 4.9 |
Ac6 | Acidobacteria; Subgroup 6 | 0.0 | 0.0 | 0.0 | 0.0 | 0.4 | 0.1 |
AcAci | Actinobacteria; Acidimicrobiia | 2.1 | 2.8 | 1.3 | 0.1 | 0.6 | 0.1 |
AcAct | Actinobacteria; Actinobacteria | 10.6 | 1.8 | 12.1 | 0.4 | 18.4 | 1.0 |
AcOt | Actinobacteria; Others | 0.6 | 20.7 | 4.6 | 0.3 | 0.2 | 0.2 |
AcTh | Actinobacteria; Thermoleophilia | 2.1 | 0.4 | 1.8 | 1.1 | 1.1 | 0.3 |
Ar | Armatimonadetes; Armatimonadia | 0.4 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
ArC | Armatimonadetes; Chthonomonadetes | 0.5 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
ArFi | Armatimonadetes; Fimbriimonadia | 0.6 | 0.0 | 0.0 | 0.0 | 0.1 | 0.0 |
Bac | Bacteroidetes; Bacteroidia | 2.6 | 0.0 | 0.2 | 0.0 | 6.1 | 0.4 |
Chl | Chloroflexi; Chloroflexia | 0.0 | 0.0 | 0.0 | 0.0 | 0.7 | 0.0 |
CyOt | Cyanobacteria; Oxyphotobacteria | 0.0 | 0.0 | 0.0 | 0.0 | 0.3 | 0.0 |
FirB | Firmicutes; Bacilli | 0.0 | 0.0 | 0.3 | 0.0 | 10.7 | 0.7 |
FirCl | Firmicutes; Clostridia | 0.0 | 0.0 | 0.0 | 0.7 | 4.9 | 1.8 |
Gem | Gemmatimonadetes; Gemmatimonadetes | 0.0 | 0.0 | 0.0 | 0.0 | 0.6 | 0.0 |
GLon | Gemmatimonadetes; Longimicrobia | 0.0 | 0.0 | 0.0 | 0.0 | 0.2 | 0.0 |
Ot | Others; Others | 13.3 | 17.5 | 2.1 | 0.6 | 1.9 | 0.4 |
PatS | Patescibacteria; Saccharimonadia | 0.0 | 0.6 | 1.3 | 0.0 | 0.1 | 0.0 |
PlPh | Planctomycetes; Phycisphaerae | 3.9 | 0.3 | 0.0 | 0.0 | 0.2 | 0.0 |
PlPl | Planctomycetes; Planctomycetacia | 5.7 | 0.0 | 0.7 | 0.0 | 0.7 | 0.0 |
ProA | Proteobacteria; Alphaproteobacteria | 9.4 | 6.3 | 9.7 | 50.2 | 24.6 | 1.7 |
ProD | Proteobacteria; Deltaproteobacteria | 2.9 | 0.6 | 0.0 | 0.0 | 1.6 | 0.1 |
ProG | Proteobacteria; Gammaproteobacteria | 12.7 | 1.6 | 1.1 | 1.8 | 17.7 | 87.5 |
ProOt | Proteobacteria; Others | 1.2 | 0.0 | 0.0 | 0.0 | 0.4 | 0.0 |
Ver | Verrucomicrobia; Verrucomicrobiae | 10.3 | 1.0 | 0.1 | 0.0 | 5.3 | 0.3 |
Parameter | Abbreviated in Figure 6 | F.1 (52.0%) | Parameter | Abbreviated in Figure 6 | F.2 (27.3%) | Parameter | Abbreviated in Figure 6 | F.3 (13.2%) |
---|---|---|---|---|---|---|---|---|
Coordinate a* according to CIE lab (red color) | a* | −0.96 | Verrucomicrobia; Verrucomicrobiae | * Ver | −0.99 | N peat | N | −0.86 |
Depth peat (negative values) | Depth | −0.94 | Proteobacteria; Deltaproteobacteria | * ProD | −0.98 | Mo peat | MoP | −0.86 |
O-alkyl C | COalk | −0.93 | Ti peat | TiP | −0.95 | P ice water | PW | −0.74 |
SUVA peat ice/water | IW SUVA | −0.88 | Proteobacteria; Others | * ProOt | −0.95 | Sr peat | SrP | 0.74 |
Coordinate b* according to CIE lab (yellow color) | b* | −0.86 | Armatimonadetes; Fimbriimonadia | * ArFi | −0.89 | Actinobacteria; Others | * AcOt | 0.81 |
L* CIE lab | L* | −0.85 | K peat | KP | −0.88 | δ15N | 15N | 0.84 |
Mg peat | MgP | −0.82 | La peat | LaP | −0.86 | C/N | C/N | 0.93 |
S peat | S | −0.82 | Proteobacteria; Gammaproteobacteria | * ProG | −0.85 | |||
P peat | PP | −0.77 | Rb peat | RbP | −0.85 | |||
Cd peat | CdP | −0.75 | V peat | VP | −0.85 | |||
Plab peat | Plab | −0.71 | Cs peat | CsP | −0.85 | |||
Maximum temperature in the horizon | MaxAn | −0.70 | Planctomycetes; Phycisphaerae | * PlPh | −0.85 | |||
Zr peat | ZrP | 0.71 | Mean temperature in the horizon | MeAn | −0.85 | |||
Mo ice water | MoW | 0.72 | Ce peat | CeP | −0.84 | |||
Nb peat | NbP | 0.76 | Mn peat | MnP | −0.84 | |||
Be ice water | BeW | 0.76 | Na peat | NaP | −0.84 | |||
U peat | UP | 0.76 | Dy peat | DyP | −0.84 | |||
aromatic C | Carom | 0.79 | δ13C peat | 13C | −0.84 | |||
B ice water | BW | 0.80 | pH ice water | IW pH | −0.84 | |||
Euryarchaeota; Methanobacteria | * EuMeth | 0.81 | Y peat | YP | −0.82 | |||
As ice water | AsW | 0.81 | Planctomycetes; Planctomycetacia | * PlPh | −0.82 | |||
carboxylic C | Ccarb | 0.82 | Pb peat | PbP | −0.82 | |||
Dy ice water | DyW | 0.82 | As peat | AsP | −0.81 | |||
Ce ice water | CeW | 0.83 | Armatimonadetes; Chthonomonadetes | * ArC | −0.80 | |||
Table 3, continued. | ||||||||
Parameter | Abbreviated in Figure 6 | F.1 (52.0%) | Parameter | Abbreviated in Figure 6 | F.2 (27.3%) | Parameter | Abbreviated in Figure 6 | F.3 (13.2%) |
Y ice water | YW | 0.83 | Armatimonadetes; Armatimonadia | * Ar | −0.80 | |||
Minimum temperature in the horizon | MinAn | 0.84 | Sb peat | SbP | −0.79 | |||
Sb ice water | SbW | 0.84 | Yb peat | YbP | −0.77 | |||
Ba peat | BaP | 0.85 | Li peat | LiP | −0.74 | |||
Cu ice water | CuW | 0.85 | Bacteroidetes; Bacteroidia | * Bac | −0.71 | |||
La ice water | LaW | 0.85 | Acidobacteria; Acidobacteriia | * Ac | 0.76 | |||
Cu peat | CuP | 0.86 | Bulk density peat | BD | 0.79 | |||
U ice water | UW | 0.88 | DIC ice water | IW DIC | 0.83 | |||
Decomposition of peat | DP | 0.89 | UV254 | UV254 | 0.84 | |||
Alkyl C | Calkyl | 0.90 | ||||||
Nb ice water | NbW | 0.90 | ||||||
Cyanobacteria; Oxyphotobacteria | * CyOt | 0.91 | ||||||
Gemmatimonadetes; Gemmatimonadetes | * Gem | 0.91 | ||||||
Thaumarchaeota; Nitrososphaeria | * ThNit | 0.91 | ||||||
Acidobacteria; Subgroup 6 | * Ac6 | 0.91 | ||||||
Chloroflexi; Chloroflexia | * Chl | 0.91 | ||||||
Zr ice peat | ZrW | 0.91 | ||||||
Yb ice peat | YbW | 0.91 | ||||||
Firmicutes; Bacilli | * FirB | 0.91 | ||||||
Cr ice peat | CrW | 0.92 | ||||||
B peat | BP | 0.92 | ||||||
Cr peat | CrP | 0.92 | ||||||
Ti ice peat | TiW | 0.93 | ||||||
Specific conductivity of peat ice waters | IW EC | 0.93 | ||||||
Mn ice peat | MnW | 0.93 | ||||||
Ba ice peat | BaW | 0.94 | ||||||
Firmicutes; Clostridia | * FirCl | 0.94 | ||||||
Parameter | Abbreviated in Figure 6 | F.1 (52.0%) | ||||||
V ice peat | VW | 0.95 | ||||||
Cs ice peat | CsW | 0.95 | ||||||
Na ice peat | NaW | 0.96 | ||||||
Ca ice peat | CaW | 0.96 | ||||||
Li ice peat | LiW | 0.96 | ||||||
Fe ice peat | FeW | 0.96 | ||||||
Mg ice peat | MgW | 0.97 | ||||||
Cd ice peat | CdW | 0.97 | ||||||
K ice peat | KW | 0.97 | ||||||
Rb ice peat | RbW | 0.98 | ||||||
Zn ice peat | ZnW | 0.98 | ||||||
Co ice peat | CoW | 0.99 | ||||||
Ni ice peat | NiW | 0.99 | ||||||
Sr ice peat | SrW | 0.99 | ||||||
DOC ice peat | IW DOC | 0.99 | ||||||
Si ice peat | SiW | 1.00 |
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Aksenov, A.S.; Shirokova, L.S.; Kisil, O.Y.; Kolesova, S.N.; Lim, A.G.; Kuzmina, D.; Pouillé, S.; Alexis, M.A.; Castrec-Rouelle, M.; Loiko, S.V.; et al. Bacterial Number and Genetic Diversity in a Permafrost Peatland (Western Siberia): Testing a Link with Organic Matter Quality and Elementary Composition of a Peat Soil Profile. Diversity 2021, 13, 328. https://doi.org/10.3390/d13070328
Aksenov AS, Shirokova LS, Kisil OY, Kolesova SN, Lim AG, Kuzmina D, Pouillé S, Alexis MA, Castrec-Rouelle M, Loiko SV, et al. Bacterial Number and Genetic Diversity in a Permafrost Peatland (Western Siberia): Testing a Link with Organic Matter Quality and Elementary Composition of a Peat Soil Profile. Diversity. 2021; 13(7):328. https://doi.org/10.3390/d13070328
Chicago/Turabian StyleAksenov, Andrey S., Liudmila S. Shirokova, Oksana Ya. Kisil, Sofiia N. Kolesova, Artem G. Lim, Darya Kuzmina, Sophie Pouillé, Marie A. Alexis, Maryse Castrec-Rouelle, Sergey V. Loiko, and et al. 2021. "Bacterial Number and Genetic Diversity in a Permafrost Peatland (Western Siberia): Testing a Link with Organic Matter Quality and Elementary Composition of a Peat Soil Profile" Diversity 13, no. 7: 328. https://doi.org/10.3390/d13070328