Physicochemical characteristics of five soda lakes
The physicochemical parameters of the samples collected from soda lakes were significantly different (Table 2). The salinity (Na+) of the samples ranged from 7.99 g/L to 68.45 g/L. The salinity (Na+) was as high as 60.00 g/L and 68.45 g/L in samples of lakes B and D, respectively, while it was medium in samples of lakes C and E, and very low in lake A (7.99 g/L), which were consistent with the conductivity data of water samples. In the samples, CO32−, Cl− and SO42− were the main anions, and their concentrations were positively correlated with salinity (Na+), which were significantly higher than those of freshwater lakes. The color of water samples of lakes B and D was pink, and other lakes were colorless. The pink lake could be explained by dense blooms of halophilic microorganism, which synthesized lots of carotenoid to adapt to the environment of low dissolved oxygen and high light intensity (Grant and Sorokin, 2011).
Table 2
Physicochemical parameters of sediment samples from five soda lakes
Sample | pH | SO42−(g/L) | Cl−(g/L) | Na+(g/L) | NO3−-N(mg/kg) | NH4+-N(mg/kg) | MC(%) | TOM(mg/kg) |
A1 | 9.22 (±0.03) | 0.54 (±0.01) | 1.63 (±0.08) | 8.28 (±0.06) | 2.85 (±0.10) | 15.14 (±0.09) | 25.21 (±0.06) | 40.92 (±0.16) |
A2 | 9.63 (±0.12) | 0.68 (±0.03) | 1.36 (±0.18) | 8.00 (±0.22) | 2.17 (±0.03) | 6.79 (±0.11) | 14.40 (±0.06) | 9.86 (±0.11) |
A3 | 9.33 (±0.33) | 0.61 (±0.01) | 1.70 (±0.10) | 7.99 (±0.09) | 8.40 (±0.09) | 19.28 (±0.14) | 23.50 (±0.11) | 14.28 (±0.03) |
B1 | 9.69 (±0.23) | 11.16 (±0.04) | 52.16 (±0.06) | 58.65 (±0.11) | 6.55 (±0.02) | 4.10 (±0.06) | 14.97 (±0.03) | 28.53 (±0.06) |
B2 | 9.49 (±0.13) | 9.23 (±0.11) | 55.34 (±0.06) | 60.00 (±0.03) | 20.02 (±0.01) | 6.32 (±0.14) | 21.44 (±0.04) | 72.01 (±0.09) |
B3 | 9.57 (±0.07) | 13.12 (±0.24) | 53.44 (±0.06) | 59.15 (±0.19) | 20.35 (±0.02) | 5.65 (±0.18) | 11.51 (±0.02) | 4.38 (±0.03) |
C1 | 9.36 (±0.02) | 7.03 (±0.05) | 15.43 (±0.03) | 28.29 (±0.07) | 4.02 (±0.06) | 0.13 (±0.10) | 10.94 (±0.23) | 4.74 (±0.17) |
C2 | 9.05 (±0.01) | 5.93 (±0.09) | 13.34 (±0.03) | 25.20 (±0.45) | 5.03 (±0.03) | 0.13 (±0.03) | 12.07 (±0.22) | 23.08 (±0.01) |
C3 | 9.35 (±0.09) | 7.71(±0.12) | 17.81 (±0.03) | 29.92 (±0.17) | 3.18 (±0.04) | 0.13 (±0.03) | 14.32 (±0.19) | 107.93 (±0.02) |
D1 | 10.05(±0.03) | 23.03 (±0.03) | 70.14 (±0.07) | 66.47 (±0.08) | 5.37 (±0.09) | 0.31 (±0.05) | 15.02 (±0.05) | 28.22 (±0.02) |
D2 | 9.12 (±0.02) | 21.00 (±0.01) | 65.17 (±0.07) | 64.49 (±0.11) | 0.1 (±0.12) | 5.00 (±0.06) | 9.75 (±0.17) | 28.39 (±0.04) |
D3 | 9.49 (±0.13) | 25.03 (±0.17) | 71.12 (±0.07) | 68.45 (±0.23) | 6.38 (±0.18) | 0.17 (±0.01) | 13.48 (±0.03) | 14.60 (±0.11) |
E1 | 9.79 (±0.12) | 2.77 (±0.16) | 5.55 (±0.13) | 21.62 (±0.04) | 1.50 (±0.12) | 6.88 (±0.01) | 17.31 (±0.08) | 5.09 (±0.16) |
E2 | 9.71 (±0.08) | 2.13 (±0.06) | 5.02 (±0.02) | 20.01 (±0.05) | 0.82 (±0.02) | 3.95 (±0.03) | 16.07 (±0.04) | 54.90 (±0.09) |
E3 | 9.38 (±0.10) | 3.49 (±0.18) | 6.15 (±0.14) | 22.65 (±0.07) | 5.20 (±0.04) | 7.69 (±0.07) | 17.30 (±0.06) | 9.48 (±0.09) |
Nitrogen content and total organic matter were also considered (Table 2). There were significant differences in concentrations of NH4+-N and NO3−-N (P<0.05, n=3), in which the NH4+-N concentration in the samples of lake A was obviously higher than that in other lakes, and the NO3−-N concentration in the samples of lake B was markedly higher. The total organic matter (TOM) of the three sampling points in the same lake was significantly different, but no obvious regularity was found. The pH of sediment samples was between 9.0-10.0. There was no significant difference in moisture content (MC) of sediment samples in the five lakes.
Bacteria Diversity In Sediment Samples
High-throughput sequencing sample description and alpha-diversity index of total bacteria (16S rRNA), SOB (soxB gene), and SRB (dsrB gene) in sediment samples were shown in Supplementary Table 1. The coverage of the sequencing libraries of all samples is over 96%, most of which reached over 99%, which could reflect the microbial community in each sample. Shannon index and Chao index were calculated. The results showed that the diversity of bacteria in most samples had little difference. However, there were some exceptions. The diversity of SOB in A1 and D3 samples and SRB in A3 sample was significantly lower than that in other samples. Table 3 summarized the correlation between diversity index and physicochemical characteristics of the samples. In all the samples, the α-diversity index of total bacteria, SOB and SRB was highly correlated with the salinity (Na+/SO42−/Cl−) and concentration of NO3−-N, while it had a low correlation with other parameters. Shannon and Chao indexs of total bacteria and SOB were negatively correlated with the salinity and concentration of NO3−-N. The Shannon and Chao indexs of SRB were positively correlated with salinity, while were negatively correlated with NO3−-N concentration. These results indicated that the diversity of total bacteria and SOB decreased with the increase of salinity, especially the total bacteria. With the increase of NO3−-N concentration, the diversity of total bacteria, SOB and SRB all decreased.
Table 3
Correlation analysis between alpha-diversity and physicochemical parameters of soda lakes
Alpha-diversity | Na+/SO42−/Cl− | NH4+-N | NO3−-N | TOM | pH | MC |
16s rRNA |
Shannon index | -0.491 | -0.269 | -0.636* | 0.011 | -0.09 | -0.139 |
Chao index | -0.633* | 0.007 | -0.568 | 0.29 | -0.306 | -0.057 |
SOB |
Shannon index | -0.316 | -0.280 | -0.361 | -0.032 | -0.088 | -0.286 |
Chao index | -0.196 | -0.358 | -0.561 | 0.032 | 0.241 | -0.343 |
SRB |
Shannon index | 0.302 | -0.364 | -0.650* | 0.056 | 0.462 | -0.203 |
Chao index | 0.151 | -0.203 | -0.727* | 0.091 | 0.256 | -0.154 |
Note: * represents significant correlation, *P<0.05 |
Total Bacterial Community In Sediment Samples
We compared and annotated sequencing results of 16s rRNA and performed taxonomic analysis on phylum level (Fig. 2A). Total bacterial community mainly included phyla Proteobacteria (11.34-46.00%), Bacteroidetes (10.10-45.24%), Halanaerobiaeota (0.03-53.53%), Firmicutes (0.73-21.95%), Actinobacteria (0.75-16.31%) and Gemmatimonadetes (0.1-17.59%). The results showed that there were quite differences in bacterial composition among the samples from different lakes. However, three samples from the same lake, with similar physicochemical parameters, had similar bacterial composition, which indicated that the physicochemical parameters were important factors affecting the bacterial composition. Meanwhile, it should be noted that the bacterial diversity of samples B and D with high salinity was lower than that of other samples, and the content of phyla Haloanaerobiaeota, which was famous for its salt tolerance and anaerobic characteristics, was significantly higher than that of other samples.
Sob Community In Sediment Samples
Many microorganisms, including obligate anaerobes, facultative anaerobes and aerobic bacteria, play roles in sulfur oxidation (Ghosh and Dam, 2009; Jung et al. 2010). Based on the results of high-throughput sequencing of soxB gene, the taxonomic composition of SOB was analyzed on genus level (Fig. 2B, Supplementary Fig. 1A), in which 26 SOB genera were detected, including Thioalkalivibrio (Gammaproteobacteria), Burkholderia and Hydrogenophaga (Betaproteobacteria), Paracoccus, Bradyrhizobium (Alphaproteobacteria) and so on. The compositions of SOB were different in the sediment samples of five soda lakes. However, the cluster of bacteria was basically consistent with the sampling sites, that was, the samples from the same lake had similar composition and proportion of SOB. On the whole, based on the annotated results, the diversity of SOB was relatively low. Thioalkalivibrio was found dominant in the majority of samples with relative abundances ranging from 0.9–81.7%. Burkholderia was only detected in the sediment samples of lakes A and E with a low salinity, and the relative abundance was the highest in the sediment samples of lake E3, which was as high as 10.3%. Paracoccus was found in a small amount of the majority of samples, while it was relatively high in lakes A and E with a low salinity, which reached 5.92%, and the abundance of Hydrogenophaga was 4.51% only in lake C. Purple non-sulfur bacteria and purple sulfur bacteria, including Rhodoplanes (0.94%) and Halorhodospira (0.58%), were detected in lake D with a high salinity.
Srb Community In Sediment Samples
Based on the results of high-throughput sequencing of dsrB gene, the taxonomic composition of SRB was analyzed at the genus level (Fig. 2C, Supplementary Fig. 1B), and it was revealed that 39 SRB genera, including Desulfurivibrio, Candidatus Electrothrix, Desulfonatronum, Desulfonatronovibrio, Desulfonatronobacter, Desulfohalophilus, Desulfonatronospira and so on, all belong to the deltaproteobacteria class. It was observed that the community structure of the SRB varied across the different soda lakes. Similar to SOB, the cluster of SRB was consistent with the sampling sites. However, compared with SOB, the diversity of SRB was higher in all samples. Desulfunvibno was detected in the majority of the samples, while it was dominant only in lake D with a high-salinity, and the relative abundance was as high as 28.09%. The relative abundances of Candidatus Electrothrix, Desulfonatronum, and Desulfonatronovibrio were relatively high in lakes A and E with a low-salinity, and the highest abundance was 38.58%, 43.20%, and 17.45%, respectively. Desulfonatronospira and Desulfohalophilus were found to have higher abundance only in lakes B and D with a high salinity, which reached 18.69% and 8.79%, respectively. Desulfonatronobacter was detected to have a higher abundance in lake B, which was as high as 22.70%.
Effects of physicochemical factors on the SOB and SRB community
To illustrate the relationship between the microbial communities and physicochemical characteristics in soda lakes, Spearman’s correlation analysis and Redundant analysis (RDA) were conducted. Spearman correlation analysis showed that most of the dominant SOB were highly correlated with the concentrations of NH4+-N and salinity (Na+) (Table 4). Specifically, Bradyrhizobium, stappia and rhodoplanes were positively correlated with salinity. Burkholderia and Paracoccus were positively correlated with NH4+-N concentration, while Bradyrhizobium and Hydrogenophaga were the opposite. In addition, Bradyrhizobium and Hydrogenophaga were significantly affected by MC. As the main SOB in the soda lake, Thioalkalivibrio was not significantly affected by the factors investigated, which indicated that Thioalkalivibrio had a wide range of adaptability. Overall, as shown in Fig. 3A, NH4+-N was the most important factor influencing the composition of SOB in the soda lake, followed by salinity.
Table 4
Correlation analysis between SOB, SRB and physicochemical parameters of soda lakes
Bacteria | Na+/SO42−/Cl− | NH4+-N | NO3−-N | TOM | pH | MC |
SOB | | | | | | |
Thioalkalivibrio | 0.164 | 0.409 | 0.196 | 0.268 | -0.111 | 0.261 |
Burkholderia | -0.497 | 0.608* | -0.436 | -0.364 | -0.192 | 0.234 |
Paracoccus | -0.065 | 0.552* | 0.062 | -0.153 | 0.044 | 0.366 |
Bradyrhizobium | 0.611* | -0.574* | -0.130 | -0.077 | 0.082 | -0.576* |
Hydrogenophaga | 0.364 | -0.566* | -0.165 | -0.133 | -0.023 | -0.545* |
Stappia | 0.560* | -0.189 | -0.005 | 0.335 | 0.046 | -0.183 |
Halorhodospira | 0.484 | -0.179 | 0.516* | -0.161 | -0.014 | -0.296 |
Rhodoplanes | 0.553* | -0.145 | -0.199 | 0.133 | 0.211 | -0.248 |
SRB | | | | | | |
Desulfurivibrio | 0.367 | -0.524 | -0.091 | 0.448 | 0.312 | -0.259 |
Candidatus Electrothrix | -0.674* | 0.711* | -0.458 | -0.366 | -0.095 | 0.394 |
Desulfonatronospira | 0.583* | -0.399 | 0.657* | 0.084 | -0.291 | -0.343 |
Desulfonatronum | -0.725** | 0.495 | -0.605* | -0.011 | 0.152 | 0.470 |
Desulfonatronovibrio | -0.429 | 0.502 | -0.573 | -0.011 | 0.027 | 0.431 |
Desulfonatronobacter | -0.194 | 0.245 | 0.490 | 0.028 | -0.091 | 0.273 |
Desulfohalophilus | 0.758** | -0.741** | 0.046 | 0.183 | 0.294 | -0.528 |
Note: * represents significant correlation, * P<0.05, ** P<0.01 |
As shown in Table 4 and Fig. 3B, the influence of physicochemical factors on SRB composition was analyzed. Similar to SOB, salinity and NH4+-N had significant effects on SRB. Candidatus electrothrix and Desulfonatronum were negatively correlated with salinity, while Desulfonatronospira and Desulfonalophilus were on the contrary. For the effect of NH4+-N, it was found that the significant effect of NH4+-N on Candidatus electrotherix was positively correlated, while the effect on Desulfohalophilus was negatively correlated. Different with SOB analysis, the effect of NO3−-N concentration on SRB was more obvious, especially on Desulfonatronospira and Desulfonatronum. Desulfurivibrio was the main SRB bacteria in soda lakes, which had strong adaptability and was not affected by environmental factors, which was similar to Thioalkalivibrio. In short, salinity was noted as the most important factor that influenced the composition of SRB, followed by the NO3−-N and NH4+-N. In addition, it can be seen from the above data that TOM, pH and MC had no significant effect on the composition of SOB and SRB.
Co-occurences Of Sob And Srb
In order to study the interaction between SOB and SRB, we used R programming language and Gephi 0.9.2 software to analyze and draw a network diagram. As shown in Fig. 4, there were 65 nodes (bacteria) and 309 edges in the graph. A group of closely associated microorganisms in the microbial network were divided into the same module. The bacterium in the same module had similar niches. The colors of different nodes denoted different modules. As shown in Fig. 4, there were 5 modules (Ⅰ-Ⅴ), and the proportion of each module was 29.23%, 18.46%, 18.46%, 15.38% and 6.15%. The network diagram showed the complex relationship between sulfur metabolizing bacteria in soda lake sediments. Most SRB were distributed in the same module (module Ⅳ), which indicated that their functions were similar and had relatively close niche. Similar to SRB, photophilic sulfur oxidizing bacteria were mostly found in module III. However, as the highest abundance of SOB, Thioalkalivibrio occupied a less important position, which implied the diversity of sulfur oxidizers and their unimportance in determining the niche.
It can be seen that Rhodoplanes was highly connected with other bacteria, which was called kinless hubs, although its relative abundance was low in the samples. Previous research had shown that the relative abundance of taxa classified as kinless hubs within the ecological network were positively and significantly correlated with the abundance of functional genes (Shi et al. 2020). The demise of kinless hubs would bring huge changes to the community structure and its functions (Banerjee et al. 2018). Rhodoplanes had a unique position in the microbial community of this study. Rhodoplanes was a kind of purple non-sulfur bacteria, which belonged to Alphaproteobacteria (Okamura et al. 2009). Rhodoplanes could grow aerobically in the atmosphere or grow anaerobically through denitrification in the dark, but the preferred growth way was to use simple organic acids, such as pyruvate, for anaerobic organic growth (Chakravarthy et al. 2012). Rhodoplanes had been reported to have an optimal pH of 7.0 (Chakravarthy et al. 2012). However, it was found that Rhodoplanes play an important role in the community of soda lake sediments, indicating the existence of some haloalkalophilic Rhodoplanes species.