Bacterial and archaeal compositions and influencing factors in soils under different submergence time in a mercury-sensitive reservoir

https://doi.org/10.1016/j.ecoenv.2019.110155Get rights and content

Highlights

  • Sediments had significantly higher bacterial and archaeal richness and α-diversities than the other three soil types.

  • Anaerolinea, Aeromonas, AltiarchaealesNitrosoarchaeum and Methanosarta dominated in SSe, sharply decreasing in others.

  • All the variables except pH posed a significant positive effect on bacterial and archaeal compositions in sediments.

  • MeHg and THg concentrations had relatively weaker effects on microbial compositions comparing to other variables.

Abstract

Soils in the water-level-fluctuating zone (WLFZ) of Three Gorges Reservoir (TGR) inundated by water for different periods of time are confirmed to have disparate characteristics to mercury (Hg), and thus it is of great significance to further investigate microbial compositions and influencing factors. The objective of this study was to compare bacterial and archaeal richness, α-diversities and compositions, as well as affecting variables, especially Hg concentrations, among soils under different submergence time—SI (inundated soil), SS (semi-inundated soil), SN(non-inundated soil) and SSe (sediment)—based on high throughput sequencing. Results showed that sediment had significantly higher bacterial and archaeal richness and α-diversities than the other soil types. Anaerolinea and Aeromonas, as well as Altiarchaeales, Nitrosoarchaeum, and Methanosarta were dominant in SSe, while sharply decreasing in the other soil types, with significant difference among groups. An unclassified genus in SCG critically predominating in SI, SS and SN, drastically reduced in SSe, with extremely significant difference among groups. Bathyarchaeota and Nitrososphaera, both dominating in SSe, decreased dramatically and almost vanished in SI and SN. All the variables except pH posed a significant positive effect on bacterial and archaeal compositions in SSe, while opposite effect in the other three soil types. MeHg and THg concentrations had relatively weaker effects on microbial compositions comparing to variables like NH4+, CEC, OM and SO42+.

Introduction

Reservoirs are different from other aquatic ecosystem in that the water level changes periodically due to artificial regulation, and a certain area of water-level-fluctuating zone (WLFZ) is formed in the drying period. Since 1980s, it has been found in North America and Europe that the concentrations of methylmercury (MeHg) in plankton, insects and fish in many new reservoirs increased significantly due to the construction of reservoirs (Abernathy and Cumbie, 1977; Lodenius et al., 1983). Therefore, new reservoirs are found to be conducive to the activation and methylation of mercury (Hg) and are considered to be a typical “Hg sensitive ecosystem” (Feng et al., 2009a; Xiang et al., 2014, 2018). The increase of MeHg caused by reservoir construction is called “reservoir effect” of Hg (Feng, 2011). Extensive research on the biogeochemical cycle of Hg in reservoirs were conducted worldwide (Eckley et al., 2017; Feng et al., 2009a, 2009b; Gray and Hines, 2009; Hecky et al., 1991; Jackson, 1988; Wasik et al., 2015). Among millions of reservoirs constructed worldwide, Three Gorges Reservoir (TGR) seems to be by far the largest annual regulation one as a world-renowned super-large project. Since its completion, its water level has been periodically adjusted and controlled up to 175 m per year, resulting in the formation of WLFZ of 30 m in vertical height and 350 km2 in area. The periodic and critically considerable fluctuation makes TGR possess conspicuous “reservoir effect” of Hg from other old reservoirs, which means TGR possesses the characteristics of Hg of new reservoirs every year (Zhao et al., 2015). More importantly, previous research has revealed that soils inundated by water for different periods of time in the WLFZ, TGR had disparate characteristics to Hg and MeHg (Du et al., 2017; He, 2013; Xiang et al., 2014, 2018). Therefore, the reservoir effect of Hg in TGR has raised great concern in the past years. In addition, the biogeochemical circle of Hg is a complex process and is confirmed to be affected by a wide variety of environmental factors, including microbial species and structures, concentrations of Hg2+ and MeHg, cation exchange capacity (CEC), base saturation (BS), organic matter (OM), pH values, Fe2+, NH4+, SO42−, etc. (Frohne et al., 2012; Merritt and Amirbahman, 2009; Ullrich et al., 2001). Currently, microbial species being confirmed to possess essential roles in biogeochemical cycle of Hg primarily include sulfate reducing bacteria (SRB), iron reducing bacteria (IRB) and methanogens, distributed mainly in δ-Proteobacteria (Parks et al., 2013; Ranchoupeyruse et al., 2009), Clostridia (Gilmour et al., 2013), and Methanobacteria (Gilmour et al., 2013, 2018; Yu et al., 2013; Podar et al., 2015). However, it is still not known that what kind of microorganisms are dominantly distributed in different soil types of the WLFZ of TGR, and how these microbial species are affected by various biogeochemical factors in reservoir ecosystem under artificial interference. Therefore, the main objective of this study is to analyze and compare dominant microorganisms in soils under different submergence time and how they are affected by biogeochemical factors, especially Hg and MeHg concentrations, in the biggest reservoirs worldwide so far.

Section snippets

Study area

Chongqing is located in the upper reaches of Yangtze River in the eastern part of Sichuan Basin, southwest China. The tested soil and sediment samples were collected from the WLFZ of Xinzheng Village, Shibao County (S for short), Zhong County, Chongqing (Fig. 1) (E108°7′41"; N30°25′40″). Previous research had demonstrated that SRB-related Hg-methylators were of higher α-diversity and abundance in Shibao County among several sites researched (Du et al., 2017), so it was selected in this research

Species richness, evenness and diversities

A total of 12 samples were sequenced on PE300 platform. The number of reads ranged from 32041 to 62665, with average length of 447.9 bp for archaea, while the number of reads for bacterial 16S rRNA sequencing ranged from 33060 to 58606, with average length of 439.7 bp. Bacteria and archaea 16S rRNA amplicon sequencing yielded 3786 and 489 OTUs based on the minimum sample sequence, which matched to 734 and 59 known genera respectively. Rarefaction curves showing relationship between the number

Conclusion

Bacterial and archaeal richness, α-diversities and compositions, as well as affecting variables among soils and sediments under different submergence time, namely inundated, semi-inundated soil and non-inundated soils, as well as sediment in a Hg-sensitive reservoir, TGR were investigated and compared based on 16S rRNA amplicon high throughput sequencing. As expected, the sediment being deeply-submerged in water throughout the whole year had significantly higher bacterial and archaeal richness

Notes

The authors declare no competing financial interest.

CRediT authorship contribution statement

Hongxia Du: Formal analysis, Writing - original draft. Tao Sun: Data curation, Methodology. Dingyong Wang: Supervision, Writing - review & editing. Ma Ming: Conceptualization, Methodology, Data curation.

Acknowledgements

This work was supported by the National Natural Science Foundation of China (No. 41603098 & 41877382), Fundamental Research Funds for the Central Universities (No. XDJK2018B043 & XDJK2019B073), Natural Science Foundation of Chongqing (No. cstc2017jcyjAX0250) and Natural Technical Innovation and Application Demonstration Project of Chongqing (No. cstc2018jscx-msybX0080).

References (64)

  • C. Liu et al.

    Evolution of microbial community along with increasing solid concentration during high-solids anaerobic digestion of sewage sludge

    Bioresource technol

    (2016)
  • M. Ma et al.

    Characteristics of archaea and bacteria in rice rhizosphere along a mercury gradient

    Sci. Total Environ.

    (2019)
  • K.A. Merritt et al.

    Mercury methylation dynamics in estuarine and coastal marine environments-a critical review

    Earth Sci. Rev.

    (2009)
  • G. Qiu et al.

    Environmental contamination of mercury from Hg-mining areas in Wuchuan, northeastern Guizhou, China

    Environ. Pollut.

    (2006)
  • C. Shen et al.

    Soil pH drives the spatial distribution of bacterial communities along elevation on Changbai Mountain

    Soil Biol. Biochem.

    (2013)
  • Y. Wang et al.

    A review of studies on the biogeochemical behaviors of mercury in the three gorges reservoir, China

    Bull. Environ. Contam. Toxicol.

    (2019)
  • Y. Xiang et al.

    Water level fluctuations influence microbial communities and mercury methylation in soils in the Three Gorges Reservoir, China

    J. Environ. Sci.

    (2018)
  • N. Xu et al.

    Effect of biochar additions to soil on nitrogen leaching, microbial biomass and bacterial community structure

    Eur. J. Soil Biol.

    (2016)
  • A.R. Abernathy et al.

    Mercury accumulation by largemouth bass (Micropterus-Salmoides) in recently impounded reservoirs

    Bull. Environ. Contam. Toxicol.

    (1977)
  • S.M. Bernasconi et al.

    Chemical and biological gradients along the damma glacier soil chronosequence, Switzerland

    Vadose Zone J.

    (2011)
  • C. Blodau et al.

    Support for an anaerobic sulfur cycle in two Canadian peatland soils

    J. Geophys. Res. Biogeosci.

    (2007)
  • J. Bori et al.

    Geochemistry and environmental threats of soils surrounding an abandoned mercury mine

    Environ. Sci. Pollut. Res.

    (2016)
  • H. Cao et al.

    Phylogenetic diversity and ecological pattern of ammonia-oxidizing archaea in the surface sediments of the western pacific

    Microb. Ecol.

    (2011)
  • T. Cerqueira et al.

    Sediment microbial diversity of three deep-sea hydrothermal vents southwest of the azores

    Microb. Ecol.

    (2017)
  • H. Chu et al.

    Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes

    Environ. Microbiol.

    (2010)
  • R.M. Cory et al.

    Surface exposure to sunlight stimulates CO2 release from permafrost soil carbon in the Arctic

    Proc. Natl. Acad. Sci.

    (2013)
  • H. Du et al.

    Mercury-methylating genes dsrB and hgcA in soils/sediments of the Three Gorges Reservoir

    Environ. Sci. Pollut. Res.

    (2017)
  • Y. Fang et al.

    Soil microbial community composition and environmental controls in northern temperate steppe of China

    Acta Sci. Nauralium Univ. Pekin.

    (2017)
  • X. Feng

    A review on mercury biogeochemical cycling in reservoirs

    Environ. Prot. Technol.

    (2011)
  • N. Fierer et al.

    Toward an ecological classification of soil bacteria

    Ecology

    (2007)
  • V.G. Fonseca et al.

    Second-generation environmental sequencing unmasks marine metazoan biodiversity

    Nat. Commun.

    (2010)
  • T. Frohne et al.

    Biogeochemical factors affecting mercury methylation rate in two contaminated floodplain soils

    Biogeosciences

    (2012)
  • Cited by (6)

    • Microbial diversity alteration reveals biomarkers of contamination in soil-river-lake continuum

      2022, Journal of Hazardous Materials
      Citation Excerpt :

      Actibacter was found significantly abundant in aquatic sediments, Thiobacillus in the river and soil compartments (LEfSe, p < 0.05), while LEfSe revealed no specific habitat for Anaerolinea (Fig. 4). Interestingly, Anaerolinea has been detected in mercury contaminated soil/water transition zone (Du et al., 2020), being more abundant in sediment than in soil. It is likely that this genus is well adapted to the variation of environmental parameters as that occurring in mixing zone such as soil-river-lake continuum.

    View full text