Soil bacterial diversity and function in semi-arid forest parks in Baotou City

doi:10.17520/biods.2022245

Abstract

Abstract:

Aim: Soil microorganisms are the main drivers of material cycling in urban park ecosystems, but there are few studies on the structure and function of forest soil bacterial communities in semi-arid urban parks.
Methods: In this study, three typical forest parks, Olympic Park (AL), Laodong Park (LD) and Aerding Botanical Garden (ZW) in Baotou City were selected, and the bacterial 16S rRNA V4-V5 regions were sequenced using Illumina high-throughput sequencing techniques to analyze the diversity, community composition and the mechanism underlying community assembly of bacteria. The metabolic functions of the bacterial community were also analyzed using Tax4Fun.
Results: The results showed that soil bacterial richness index were LD (2,443.00 ± 9.37) > ZW (2,392.90 ± 8.23) > AL (2,305.57 ± 17.48). Actinobacteriota, Proteobacteria, Acidobacteriota, Chloroflexi, and Gemmatimonadota were the dominant phyla. Bacterial community composition differed significantly among the three parks, and linear discriminant analysis effect size (LEfSe) results indicated that all parks harbored significant opertational taxonomic units in abundance. The neutral community model (NCM), normalized stochasticity ratio (NST), and the infer community assembly mechanisms by phylogenetic-bin-based null model analysis (iCAMP) showed that community assembly of bacteria in urban forests was determined by the combination of stochastic and deterministic processes, with drift and homogeneous selection being the dominant ecological processes. The results of Tax4Fun functional prediction indicated that metabolism involving membrane transport, carbohydrate metabolism, amino acid metabolism, energy metabolism and signal transduction were the main metabolic functions of soil bacteria in these urban parks, and further analysis showed that the metabolic functions of microbial communities differed across parks.
Conclusion: Our study investigated preliminarily the diversities, community assembly mechanisms and functions of bacteria in the semi-arid urban parks, which could provide basic data and scientific basis for urban park green space construction and ecological improvement.

Key words: semi-arid city, park understory soil, bacterial community, construction mechanism, function prediction

Xuan Zhang, Wei Du, Ying Xu, Yonglong Wang. Soil bacterial diversity and function in semi-arid forest parks in Baotou City[J]. Biodiv Sci, 2022, 30(7): 22245.

Add to citation manager EndNote|Ris|BibTeX

URL: https://www.biodiversity-science.net/EN/10.17520/biods.2022245

https://www.biodiversity-science.net/EN/Y2022/V30/I7/22245

Figures/Tables 7

Fig. 1 Alpha diversity of soil bacteria in three forest parks in Baotou City. (a) Species accumulation curves; (b) Richness index, * indicates Wilcoxon test P < 0.05. AL, Olympic Park; LD, Laodong Park; ZW, Aerding Botanical Garden.

Fig. 2 Relative abundance of top 15 phyla and families of soil bacterial communities. (a) Phylum level, (b) Family level. AL, Olympic Park; LD, Laodong Park; ZW, Aerding Botanical Garden.

Fig. 3 Composition of soil bacterial communities in three forest parks in Baotou City. (a) Nonmetric multi-dimensional scaling (NMDS) analysis ranking analysis of bacterial communities based on Bray-Curtis distances. (b) Redundancy analysis (RDA) of soil bacteria and soil physicochemical. AP, Available phosphorus; AK, Available kalium; AN, Available nitrogen; AL, Olympic Park; LD, Laodong Park; ZW, Aerding Botanical Garden.

Fig. 4 Differences in soil bacterial communities based on operational taxonomic units (OTUs) levels (linear discriminant analysis effect size: LDA > 3, P < 0.05). AL, Olympic Park; LD, Laodong Park; ZW, Aerding Botanical Garden.

Fig. 5 Ecological processes in soil bacterial communities. Neutral community model (NCM) of soil bacteria in Olympic Park (a), Labor Park (c) and Aerding Botanical Garden (c); (d) The normalized stochasticity ratio (NST) in the three parks.

Fig. 6 The relative importance of ecological processes in soil bacterial community assembly. The importance of ecological processes was indicated by infer community assembly mechanisms by phylogenetic-bin-based null model analysis (iCAMP), (a) AL, Olympic Park; (b) LD, Laodong Park; (c) ZW, Aerding Botanical Garden. HeS, Heterogeneous selection, HoS, Homogeneous selection, HD, Homogenizing dispersal, DL, Dispersal limitation, DR, Drift.

Fig.7 Differences in soil bacterial metabolic functions. * indicates Kruskal-Wallis P < 0.05. AL, Olympic Park; LD, Laodong Park; ZW, Aerding Botanical Garden. Scale bar is normalized value of metabolic relative abundance.

References 51

[1]	Aßhauer KP, Wemheuer B, Daniel R, Meinicke P (2015) Tax4Fun: Predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics, 31, 2882-2884. DOI URL
[2]	Bahram M, Kohout P, Anslan S, Harend H, Abarenkov K, Tedersoo L (2016) Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment. The ISME Journal, 10, 885-896. DOI URL
[3]	Chase JM (2010) Stochastic community assembly causes higher biodiversity in more productive environments. Science, 328, 1388-1391. DOI URL
[4]	Chen WD, Ren KX, Isabwe A, Chen HH, Liu M, Yang J (2019) Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons. Microbiome, 7, 1-16. DOI URL
[5]	Delgado-Baquerizo M, Eldridge DJ, Liu YR, Sokoya B, Wang JT, Hu HW, He JZ, Bastida F, Moreno JL, Bamigboye AR, Blanco-Pastor JL, Cano-Díaz C, Illán JG, Makhalanyane TP, Siebe C, Trivedi P, Zaady E, Verma JP, Wang L, Wang JY, Grebenc T, Peñaloza-Bojacá GF, Nahberger TU, Teixido AL, Zhou XQ, Berdugo M, Duran J, Rodríguez A, Zhou XB, Alfaro F, Abades S, Plaza C, Rey A, Singh BK, Tedersoo L, Fierer N (2021) Global homogenization of the structure and function in the soil microbiome of urban greenspaces. Science Advances, 7, eabg5809. DOI URL
[6]	Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27, 2194-2200. DOI URL
[7]	Falkowski PG, Fenchel T, Delong EF (2008) The microbial engines that drive Earth’s biogeochemical cycles. Science, 320, 1034-1039. DOI PMID
[8]	Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology, 88, 1354-1364. PMID
[9]	Grönroos M, Parajuli A, Laitinen OH, Roslund MI, Vari HK, Hyöty H, Puhakka R, Sinkkonen A (2019) Short-term direct contact with soil and plant materials leads to an immediate increase in diversity of skin microbiota. MicrobiologyOpen, 8, e00645. DOI URL
[10]	Hanski I, von Hertzen L, Fyhrquist N, Koskinen K, Torppa K, Laatikainen T, Karisola P, Auvinen P, Paulin L, Mäkelä MJ, Vartiainen E, Kosunen TU, Alenius H, Haahtela T (2012) Environmental biodiversity, human microbiota, and allergy are interrelated. Proceedings of the National Academy of Sciences, USA, 109, 8334-8339.
[11]	Hanski I, von Hertzen L, Fyhrquist N, Koskinen K, Torppa K, Laatikainen T, Karisola P, Auvinen P, Paulin L, Mäkelä MJ, Vartiainen E, Kosunen TU, Alenius H, Haahtela T (2012) Environmental biodiversity, human microbiota, and allergy are interrelated. Proceedings of the National Academy of Sciences, USA, 109, 8334-8339.
[12]	He Q, Wang S, Hou WG, Feng K, Li FR, Hai WM, Zhang YD, Sun YX, Deng Y (2021) Temperature and microbial interactions drive the deterministic assembly processes in sediments of hot springs. Science of the Total Environment, 772, 145465. DOI URL
[13]	He RJ, Zeng J, Zhao DY, Wang SR, Wu QL (2022) Decreased spatial variation and deterministic processes of bacterial community assembly in the rhizosphere of Phragmites australis across the Middle-Lower Yangtze plain. Molecular Ecology, 31, 1180-1195. DOI URL
[14]	Hubbell SP (1979) Tree dispersion, abundance, and diversity in a tropical dry forest. Science, 203, 1299-1309. PMID
[15]	Hubbell SP (2001) The Uniﬁed Neutral Theory of Biodiversity and Biogeography, Princeton University Press, Princeton.
[16]	Hui N, Jumpponen A, Francini G, Kotze DJ, Liu XX, Romantschuk M, Strömmer R, Setälä H (2017) Soil microbial communities are shaped by vegetation type and park age in cities under cold climate. Environmental Microbiology, 19, 1281-1295. DOI URL
[17]	Jenkins JR, Viger M, Arnold EC, Harris ZM, Ventura M, Miglietta F, Girardin C, Edwards RJ, Rumpel C, Fornasier F, Zavalloni C, Tonon G, Alberti G, Taylor G (2017) Biochar alters the soil microbiome and soil function: Results of next-generation amplicon sequencing across Europe. GCB Bioenergy, 9, 591-612. DOI URL
[18]	Jiao S, Zhang BG, Zhang GZ, Chen WM, Wei GH (2021) Stochastic community assembly decreases soil fungal richness in arid ecosystems. Molecular Ecology, 30, 4338-4348. DOI URL
[19]	Lai JS, Zou Y, Zhang JL, Peres-Neto PR (2022) Generalizing hierarchical and variation partitioning in multiple regression and canonical analyses using the rdacca.hp R package. Methods in Ecology and Evolution, 13, 782-788. DOI URL
[20]	le Chatelier E, Nielsen T, Qin JJ, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li JH, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T, Bork P, Wang J, Ehrlich SD, Pedersen O (2013) Richness of human gut microbiome correlates with metabolic markers. Nature, 500, 541-546. DOI URL
[21]	Li JX, Hong M, Yin XQ, Liu JL (2010) Effects of the accumulation of the rare earth elements on soil macrofauna community. Journal of Rare Earths, 28, 957-964. DOI URL
[22]	Lin YB, Ye YM, Liu SC, Wen JH, Chen DL (2022) Effect mechanism of land consolidation on soil bacterial community: A case study in Eastern China. International Journal of Environmental Research and Public Health, 19, 845. DOI URL
[23]	Liu NN, Hu HF, Ma WH, Deng Y, Wang QG, Luo A, Meng JH, Feng XJ, Wang ZH (2021) Relative importance of deterministic and stochastic processes on soil microbial community assembly in temperate grasslands. Microorganisms, 9, 1929. DOI URL
[24]	Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS (2002) Microbial cellulose utilization: Fundamentals and biotechnology. Microbiology and Molecular Biology Reviews, 66, 506- 577. DOI PMID
[25]	Ning DL, Deng Y, Tiedje JM, Zhou JZ (2019) A general framework for quantitatively assessing ecological stochasticity. Proceedings of the National Academy of Sciences, USA, 116, 16892-16898.
[26]	Ning DL, Yuan MT, Wu LW, Zhang Y, Guo X, Zhou XS, Yang YF, Arkin AP, Firestone MK, Zhou JZ (2020) A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming. Nature Communications, 11, 1-12. DOI URL
[27]	O’Brien SL, Gibbons SM, Owens SM, Hampton-Marcell J, Johnston ER, Jastrow JD, Gilbert JA, Meyer F, Antonopoulos DA (2016) Spatial scale drives patterns in soil bacterial diversity. Environmental Microbiology, 18, 2039-2051. DOI URL
[28]	Ortiz G, Yagüe G, Segovia M, Catalán V (2009) A study of air microbe levels in different areas of a hospital. Current Microbiology, 59, 53-58. DOI URL
[29]	Pankratov TA, Ivanova AO, Dedysh SN, Liesack W (2011) Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat. Environmental Microbiology, 13, 1800-1814. DOI PMID
[30]	Ren Y, Han C, Yang H, Wei YB, Cao SY, Qian YJ, Tang Y (2021) Study on soil microbial diversity under five urban landscape plants. Soils, 53, 746-754. (in Chinese with English abstract)
	[ 任一, 韩畅, 杨慧, 魏岩冰, 曹舒阳, 钱宇杰, 唐赟 (2021) 城市五种景观植物土壤微生物多样性研究. 土壤, 53, 746-754.]
[31]	Rognes T, Flouri T, Nichols B, Quince C, Mahé F (2016) VSEARCH: A versatile open source tool for metagenomics. PeerJ, 4, e2584. DOI URL
[32]	Selway CA, Mills JG, Weinstein P, Skelly C, Yadav S, Lowe A, Breed MF, Weyrich LS (2020) Transfer of environmental microbes to the skin and respiratory tract of humans after urban green space exposure. Environment international, 145, 106084. DOI URL
[33]	Shade A, Gregory Caporaso J, Handelsman J, Knight R, Fierer N (2013) A meta-analysis of changes in bacterial and archaeal communities with time. The ISME Journal, 7, 1493-1506. DOI URL
[34]	Si WT, Liu JM, Cai L, Jiang HM, Zheng CL, He XY, Wang JY, Zhang XF (2015) Health risks of metals in contaminated farmland soils and spring wheat irrigated with Yellow River water in Baotou, China. Bulletin of Environmental Contamination and Toxicology, 94, 214-219. DOI URL
[35]	Sloan WT, Lunn M, Woodcock S, Head IM, Nee S, Curtis TP (2006) Quantifying the roles of immigration and chance in shaping prokaryote community structure. Environmental Microbiology, 8, 732-740. DOI URL
[36]	Stevenson A, Hallsworth JE (2014) Water and temperature relations of soil Actinobacteria. Environmental Microbiology Reports, 6, 744-755. DOI PMID
[37]	Sun YZ, Zhang MJ, Duan CX, Cao N, Jia WQ, Zhao ZL, Ding CF, Huang Y, Wang J (2021) Contribution of stochastic processes to the microbial community assembly on field- collected microplastics. Environmental Microbiology, 23, 6707-6720. DOI URL
[38]	Tan XL, Kan L, Zhang L, Zheng JY (2019) Seasonal dynamics of soil microbial community structure in urban forest. Chinese Journal of Ecology, 38, 3306-3312. (in Chinese with English abstract)
	[ 谭雪莲, 阚蕾, 张璐, 郑嘉仪 (2019) 城市森林土壤微生物群落结构的季节变化. 生态学杂志, 38, 3306-3312.]
[39]	Tilman D (2004) Niche tradeoffs, neutrality, and community structure: A stochastic theory of resource competition, invasion, and community assembly. Proceedings of the National Academy of Sciences, USA, 101, 10854-10861.
[40]	Wagg C, Bender SF, Widmer F, van der Heijden MGA (2014) Soil biodiversity and soil community composition determine ecosystem multifunctionality. Proceedings of the National Academy of Sciences, USA, 111, 5266-5270.
[41]	Wang XJ, Zhang ZC, Yu ZQ, Shen GF, Cheng HF, Tao S (2020) Composition and diversity of soil microbial communities in the alpine wetland and alpine forest ecosystems on the Tibetan Plateau. Science of the Total Environment, 747, 141358. DOI URL
[42]	Wei F, Passey T, Xu XM (2016) Amplicon-based metabarcoding reveals temporal response of soil microbial community to fumigation-derived products. Applied Soil Ecology, 103, 83-92. DOI URL
[43]	Xian WD, Zhang XT, Li WJ (2020) Research status and prospect on bacterial phylum Chloroﬂexi. Acta Microbiologica Sinica, 60, 1801-1820. (in Chinese)
	[ 鲜文东, 张潇橦, 李文均 (2020) 绿弯菌的研究现状及展望. 微生物学报, 60, 1801-1820.]
[44]	Xu QC, Vandenkoornhuyse P, Li L, Guo JJ, Zhu C, Guo SW, Ling N, Shen QR,(2021) Microbial generalists and specialists differently contribute to the community diversity in farmland soils. Journal of Advanced Research, doi: 10.1016/j.jare.2021.12.003. DOI
[45]	Yan X, Luo XG, Zhao M (2016) Metagenomic analysis of microbial community in uranium-contaminated soil. Applied Microbiology and Biotechnology, 100, 299-310. DOI URL
[46]	Yang JH, Wang CL, Dai HL (2008) Soil Agrochemical Analysis and Environmental Monitoring, China Earth Press, Beijing in Chinese.
	[ 杨剑虹, 王成林, 代亨林 (2008) 土壤农化分析与环境监测. 中国大地出版社, 北京.]
[47]	Zeng QC, An SS, Liu Y, Wang HL, Wang Y (2019) Biogeography and the driving factors affecting forest soil bacteria in an arid area. Science of the Total Environment, 680, 124- 131. DOI URL
[48]	Zhang JD (2019) Study of Soil Physicochemical Properties and Bacterial Community Structure of Urban Green Spaces in Beijing. PhD dissertation, Beijing Forestry University, Beijing. (in Chinese with English abstract)
	[ 张骏达 (2019) 北京市城区绿地土壤理化性质及细菌群落结构研究. 博士学位论文, 北京林业大学, 北京,.]
[49]	Zhang JD, Li SY, Sun XY, Tong J, Fu Z, Li J (2019) Sustainability of urban soil management: Analysis of soil physicochemical properties and bacterial community structure under different green space types. Sustainability, 11, 1395. DOI URL
[50]	Zhang JD, Li SY, Sun XY, Zhang H, Hu N, Fu Z, Guo ZT (2019) Analysis of soil bacterial diversity in urban parks with different ages by high throughput sequencing. Microbiology China, 46, 65-74. (in Chinese with English abstract)
	[ 张骏达, 李素艳, 孙向阳, 张骅, 呼诺, 傅振, 郭子腾 (2019) 基于高通量测序技术的不同年代公园绿地土壤细菌多样性. 微生物学通报, 46, 65-74.]
[51]	Zheng JF, Chen JH, Pan GX, Wang GM, Liu XY, Zhang XH, Li LQ, Bian RJ, Cheng K, Zheng JW (2017) A long-term hybrid poplar plantation on cropland reduces soil organic carbon mineralization and shifts microbial community abundance and composition. Applied Soil Ecology, 111, 94-104. DOI URL