Different response of bacterial community to the changes of nutrients and pollutants in sediments from an urban river network
Fang Zhang1, Hao Zhang1, Ying Yuan1, Dun Liu1, Chenyu Zhu1, Di Zheng1, Guanghe Li1, Yuquan Wei2(), Dan Sun3()
1. School of Environment and State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, China 2. College of Resource and Environmental Science, China Agricultural University, Beijing 100193, China 3. Ocean College, Zhejiang University, Zhoushan 316021, China
• Bacterial community varied spatially in sediments from the urban river network.
• Key environmental factors shaping bacterial community were detected by RDA.
• Bacterial co-occurrence networks changed at different levels of nutrient and metal.
• Potential indicator species were selected to predict pollution risk in sediment.
Microbial communities in sediment are an important indicator linking to environmental pollution in urban river systems. However, how the diversity and structure of bacterial communities in sediments from an urban river network respond to different environmental factors has not been well studied. The goal of this study was to understand the patterns of bacterial communities in sediments from a highly dense urbanized river network in the lower Yangtze River Delta by Illumina MiSeq sequencing. The correlations between bacterial communities, the environmental gradient and geographical distance were analyzed by redundancy analysis (RDA) and network methods. The diversity and richness of bacterial community in sediments increased from upstream to downstream consistently with the accumulation of nutrient in the urban river network. Bacterial community composition and structure showed obvious spatial changes, leading to two distinct groups, which were significantly related to the characteristics of nutrient and heavy metal in sediments. Humic substance, available nitrogen, available phosphorus, Zn, Cu, Hg and As were selected as the key environmental factors shaping the bacterial community in sediments based on RDA. The co-occurrence patterns of bacterial networks showed that positive interaction between bacterial communities increased but the connectivity among bacterial genera and stability of sediment ecosystem reduced under a higher content of nutrient and heavy metal in average. The sensitive and ubiquitous taxa with an overproportional response to key environmental factors were detected as indicator species, which provided a novel method for the prediction of the pollution risk of sediment in an urban river network.
. [J]. Frontiers of Environmental Science & Engineering, 2020, 14(2): 28.
Fang Zhang, Hao Zhang, Ying Yuan, Dun Liu, Chenyu Zhu, Di Zheng, Guanghe Li, Yuquan Wei, Dan Sun. Different response of bacterial community to the changes of nutrients and pollutants in sediments from an urban river network. Front. Environ. Sci. Eng., 2020, 14(2): 28.
A Alvarez, J M Saez, J S Davila Costa, V L Colin, M S Fuentes, S A Cuozzo, C S Benimeli, M A Polti, M J Amoroso (2017). Actinobacteria: Current research and perspectives for bioremediation of pesticides and heavy metals. Chemosphere, 166: 41–62 https://doi.org/10.1016/j.chemosphere.2016.09.070
pmid: 27684437
2
A Barberán, S T Bates, E O Casamayor, N Fierer (2012). Using network analysis to explore co-occurrence patterns in soil microbial communities. The ISME journal, 6(2): 343–351 https://doi.org/10.1038/ismej.2011.119
pmid: 21900968
3
L Cai, T B Chen, D Gao, J Yu (2016). Bacterial communities and their association with the bio-drying of sewage sludge. Water Research, 90: 44–51 PMID:26724438 https://doi.org/10.1016/j.watres.2015.12.026
4
X Chen, R Liu, J Hao, D Li, Z Wei, R Teng, B Sun (2019). Protein and carbohydrate drive microbial responses in diverse ways during different animal manures composting. Bioresource Technology, 271: 482–486 https://doi.org/10.1016/j.biortech.2018.09.096
pmid: 30253897
5
Y Dai, Y Yang, Z Wu, Q Feng, S Xie, Y Liu (2016). Spatiotemporal variation of planktonic and sediment bacterial assemblages in two plateau freshwater lakes at different trophic status. Applied Microbiology and Biotechnology, 100(9): 4161–4175 https://doi.org/10.1007/s00253-015-7253-2
pmid: 26711281
6
F T de Vries, R I Griffiths, M Bailey, H Craig, M Girlanda, H S Gweon, S Hallin, A Kaisermann, A M Keith, M Kretzschmar, P Lemanceau, E Lumini, K E Mason, A Oliver, N Ostle, J I Prosser, C Thion, B Thomson, R D Bardgett (2018). Soil bacterial networks are less stable under drought than fungal networks. Nature Communications, 9(1): 3033 https://doi.org/10.1038/s41467-018-05516-7
pmid: 30072764
7
Y Deng, P Zhang, Y Qin, Q Tu, Y Yang, Z He, C W Schadt, J Zhou (2016). Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation. Environmental Microbiology, 18(1): 205–218 https://doi.org/10.1111/1462-2920.12981
pmid: 26177312
8
K E Giller, E Witter, S P McGrath (1998). Toxicity of heavy metals to microorganisms and microbial processes in agricultural soils: A review. Soil Biology and Biochemistry, 30(10-11): 1389–1414 https://doi.org/10.1016/S0038-0717(97)00270-8
D R Griffith, R T Barnes, P A Raymond (2009). Inputs of fossil carbon from wastewater treatment plants to U.S. rivers and oceans. Environmental Science & Technology, 43(15): 5647–5651 https://doi.org/10.1021/es9004043
pmid: 19731657
11
M Hartmann, C G Howes, D VanInsberghe, H Yu, D Bachar, R Christen, R Henrik Nilsson, S J Hallam, W W Mohn (2012). Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests. The ISME Journal, 6(12): 2199–2218 https://doi.org/10.1038/ismej.2012.84
pmid: 22855212
12
A M Ibekwe, J Ma, S E Murinda (2016). Bacterial community composition and structure in an Urban River impacted by different pollutant sources. Science of the Total Environment, 566-567: 1176–1185 https://doi.org/10.1016/j.scitotenv.2016.05.168
pmid: 27267715
13
M Jeanbille, J Gury, R Duran, J Tronczynski, H Agogué, O Ben Saïd, J F Ghiglione, J C Auguet (2016). Response of core microbial consortia to chronic hydrocarbon contaminations in coastal sediment habitats. Frontiers in Microbiology, 7: 1637 https://doi.org/10.3389/fmicb.2016.01637
pmid: 27790213
14
C J Krebs (1999). Ecological Methodology. Menlo Park, CA: Benjamin/Cummings
15
K W Kwok, G E Batley, R J Wenning, L Zhu, M Vangheluwe, S Lee (2014). Sediment quality guidelines: Challenges and opportunities for improving sediment management. Environmental Science and Pollution Research International, 21(1): 17–27 https://doi.org/10.1007/s11356-013-1778-7
pmid: 23673922
16
C Lamanna, B Blonder, C Violle, N J B Kraft, B Sandel, I Šímová, J C Donoghue 2nd, J C Svenning, B J McGill, B Boyle, V Buzzard, S Dolins, P M Jørgensen, A Marcuse-Kubitza, N Morueta-Holme, R K Peet, W H Piel, J Regetz, M Schildhauer, N Spencer, B Thiers, S K Wiser, B J Enquist (2014). Functional trait space and the latitudinal diversity gradient. Proceedings of the National Academy of Sciences of the United States of America, 111(38): 13745–13750 https://doi.org/10.1073/pnas.1317722111
pmid: 25225365
17
Q Li, X Xu, Y Fang, R Xiao, D Wang, W Zhong (2018). The temporal changes of the concentration level of typical toxic organics in the river sediments around Beijing. Frontiers of Environmental Science & Engineering, 12(6): 8 https://doi.org/10.1007/s11783-018-1054-7
18
T Liu, A N Zhang, J Wang, S Liu, X Jiang, C Dang, T Ma, S Liu, Q Chen, S Xie, T Zhang, J Ni (2018). Integrated biogeography of planktonic and sedimentary bacterial communities in the Yangtze River. Microbiome, 6(1): 16 https://doi.org/10.1186/s40168-017-0388-x
pmid: 29351813
19
Q Lu, Y Zhao, X Gao, J Wu, H Zhou, P Tang, Q Wei, Z Wei (2018). Effect of tricarboxylic acid cycle regulator on carbon retention and organic component transformation during food waste composting. Bioresource Technology, 256: 128–136 https://doi.org/10.1016/j.biortech.2018.01.142
pmid: 29433047
20
R Lu (2000). Soil Agricultural Chemical Analysis Method. Beijing: China Agricultural Science and Technology Press, 1–315
21
L Ma, Y Liu, J Zhang, Q Yang, G Li, D Zhang (2018). Impacts of irrigation water sources and geochemical conditions on vertical distribution of pharmaceutical and personal care products (PPCPs) in the vadose zone soils. Science of the Total Environment, 626: 1148–1156 https://doi.org/10.1016/j.scitotenv.2018.01.168
pmid: 29898521
22
D D MacDonald, C G Ingersoll, T A Berger (2000). Development and evaluation of consensus-based sediment quality guidelines for freshwater ecosystems. Archives of Environmental Contamination and Toxicology, 39(1): 20–31 https://doi.org/10.1007/s002440010075
pmid: 10790498
23
L Miao, P Wang, C Wang, J Hou, Y Yao, J Liu, B Lv, Y Yang, G You, Y Xu, Z Liu, S Liu (2018). Effect of TiO2 and CeO2 nanoparticles on the metabolic activity of surficial sediment microbial communities based on oxygen microelectrodes and high-throughput sequencing. Water Research, 129: 287–296 https://doi.org/10.1016/j.watres.2017.11.014
pmid: 29156393
24
D Persaud, R Jaagumagi, A Hayton (1993). Guidelines for the protection and management of aquatic sediment quality in Ontario. Water Resources Branch. Toronto: Ontario Ministry of the Environment
25
L Qiu, H Cui, J Wu, B Wang, Y Zhao, J Li, L Jia, Z Wei (2016). Snowmelt-driven changes in dissolved organic matter and bacterioplankton communities in the Heilongjiang watershed of China. Science of the Total Environment, 556: 242–251 https://doi.org/10.1016/j.scitotenv.2016.02.199
pmid: 26974572
26
J R Rouquette, M Dallimer, P R Armsworth, K J Gaston, L Maltby, P H Warren (2013). Species turnover and geographic distance in an urban river network. Diversity and Distributions, 19(11): 1429–1439 https://doi.org/10.1111/ddi.12120
27
P D Schloss, S L Westcott, T Ryabin, J R Hall, M Hartmann, E B Hollister, R A Lesniewski, B B Oakley, D H Parks, C J Robinson, J W Sahl, B Stres, G G Thallinger, D J Van Horn, C F Weber (2009). Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 75(23): 7537–7541 https://doi.org/10.1128/AEM.01541-09
pmid: 19801464
M Y Sun, K A Dafforn, E L Johnston, M V Brown (2013). Core sediment bacteria drive community response to anthropogenic contamination over multiple environmental gradients. Environmental Microbiology, 15(9): 2517–2531 https://doi.org/10.1111/1462-2920.12133
pmid: 23647974
30
K H Tan (2014). Humic matter in soil and the environment: principles and controversies. Boca Raton: CRC Press.
31
I Vanwonterghem, P D Jensen, P G Dennis, P Hugenholtz, K Rabaey, G W Tyson (2014). Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters. The ISME Journal, 8(10): 2015–2028 https://doi.org/10.1038/ismej.2014.50
pmid: 24739627
32
L Wang, J Shen, C K L Chung (2015b). City profile: Suzhou: A Chinese city under transformation. Cities (London, England), 44: 60–72 https://doi.org/10.1016/j.cities.2014.12.005
33
L Wang, J Zhang, H Li, H Yang, C Peng, Z Peng, L Lu (2018). Shift in the microbial community composition of surface water and sediment along an urban river. Science of the Total Environment, 627: 600–612 https://doi.org/10.1016/j.scitotenv.2018.01.203
pmid: 29426184
34
Y B Wang, C W Liu, Y H Kao, C S Jang (2015a). Characterization and risk assessment of PAH-contaminated river sediment by using advanced multivariate methods. Science of the Total Environment, 524-525: 63–73 https://doi.org/10.1016/j.scitotenv.2015.04.019
pmid: 25889545
35
Y Wei, Z Wei, Z Cao, Y Zhao, X Zhao, Q Lu, X Wang, X Zhang (2016). A regulating method for the distribution of phosphorus fractions based on environmental parameters related to the key phosphate-solubilizing bacteria during composting. Bioresource Technology, 211: 610–617 https://doi.org/10.1016/j.biortech.2016.03.141
pmid: 27043056
36
Y Wei, D Wu, D Wei, Y Zhao, J Wu, X Xie, R Zhang, Z Wei (2019). Improved lignocellulose-degrading performance during straw composting from diverse sources with actinomycetes inoculation by regulating the key enzyme activities. Bioresource Technology, 271: 66–74 https://doi.org/10.1016/j.biortech.2018.09.081
pmid: 30265954
37
Y Wei, Y Zhao, M Shi, Z Cao, Q Lu, T Yang, Y Fan, Z Wei (2018). Effect of organic acids production and bacterial community on the possible mechanism of phosphorus solubilization during composting with enriched phosphate-solubilizing bacteria inoculation. Bioresource Technology, 247: 190–199 https://doi.org/10.1016/j.biortech.2017.09.092
pmid: 28950126
38
N Wéry, C Lhoutellier, F Ducray, J P Delgenès, J J Godon (2008). Behaviour of pathogenic and indicator bacteria during urban wastewater treatment and sludge composting, as revealed by quantitative PCR. Water Research, 42(1-2): 53–62 https://doi.org/10.1016/j.watres.2007.06.048
pmid: 17659319
39
J Wu, H Qi, X Huang, D Wei, Y Zhao, Z Wei, Q Lu, R Zhang, T Tong (2018). How does manganese dioxide affect humus formation during bio-composting of chicken manure and corn straw? Bioresource Technology, 269: 169–178 https://doi.org/10.1016/j.biortech.2018.08.079
pmid: 30172180
40
J Wu, Y Zhao, W Zhao, T Yang, X Zhang, X Xie, H Cui, Z Wei (2017). Effect of precursors combined with bacteria communities on the formation of humic substances during different materials composting. Bioresource Technology, 226: 191–199 https://doi.org/10.1016/j.biortech.2016.12.031
pmid: 27997873
41
Z Yan, Z Hao, H Wu, H Jiang, M Yang, C Wang (2019). Co-occurrence patterns of the microbial community in polycyclic aromatic hydrocarbon-contaminated riverine sediments. Journal of Hazardous Materials, 367: 99–108 https://doi.org/10.1016/j.jhazmat.2018.12.071
pmid: 30594728
42
J Yang, G Li, Y Qian, Y Yang, F Zhang (2018). Microbial functional gene patterns related to soil greenhouse gas emissions in oil contaminated areas. Science of the Total Environment, 628-629: 94–102 https://doi.org/10.1016/j.scitotenv.2018.02.007
pmid: 29428864
43
K Yang, L Zhu, Y Zhao, Z Wei, X Chen, C Yao, Q Meng, R Zhao (2019). A novel method for removing heavy metals from composting system: The combination of functional bacteria and adsorbent materials. Bioresource Technology, 293: 122095 https://doi.org/10.1016/j.biortech.2019.122095
pmid: 31494435
44
H Yu, Y Zhao, C Zhang, D Wei, J Wu, X Zhao, J Hao, Z Wei (2019). Driving effects of minerals on humic acid formation during chicken manure composting: Emphasis on the carrier role of bacterial community. Bioresource Technology, 294: 122239 https://doi.org/10.1016/j.biortech.2019.122239
pmid: 31610491
45
Z Yu, H Deng, D Wang, M Ye, Y Tan, Y Li, Z Chen, S Xu (2013). Nitrous oxide emissions in the Shanghai river network: Implications for the effects of urban sewage and IPCC methodology. Global Change Biology, 19(10): 2999–3010 https://doi.org/10.1111/gcb.12290
pmid: 23907853
46
H Zhang, Y Jiang, M Ding, Z Xie (2017). Level, source identification, and risk analysis of heavy metal in surface sediments from river-lake ecosystems in the Poyang Lake, China. Environmental Science and Pollution Research International, 24(27): 21902–21916 https://doi.org/10.1007/s11356-017-9855-y
pmid: 28780687
47
H Zhang, Z Wan, M Ding, P Wang, X Xu, Y Jiang (2018). Inherent bacterial community response to multiple heavy metals in sediment from river-lake systems in the Poyang Lake, China. Ecotoxicology and Environmental Safety, 165: 314–324 https://doi.org/10.1016/j.ecoenv.2018.09.010
pmid: 30212732
48
J Zhang, L H Wang, J C Yang, H Liu, J L Dai (2015). Health risk to residents and stimulation to inherent bacteria of various heavy metals in soil. Science of the Total Environment, 508: 29–36 https://doi.org/10.1016/j.scitotenv.2014.11.064
pmid: 25437950
49
X Zhang, Q Gu, X E Long, Z L Li, D X Liu, D H Ye, C Q He, X Y Liu, K Väänänen, X P Chen (2016). Anthropogenic activities drive the microbial community and its function in urban river sediment. Journal of Soils and Sediments, 16(2): 716–725 https://doi.org/10.1007/s11368-015-1246-8
