Differential response patterns of soil fungal and bacterial communities to typical vegetation types in the Yellow River floodplain ecosystem

References

• Behr JH, Kampouris ID, Babin D, Sommermann L, Francioli D, Kuhl-Nagel T, Chowdhury SP, Geistlinger J, Smalla K, Neumann G, et al. 2023. Beneficial microbial consortium improves winter rye performance by modulating bacterial communities in the rhizosphere and enhancing plant nutrient acquisition. Front Plant Sci. 14:1. doi: 10.3389/fpls.2023.1232288.
   Web of Science ®Google Scholar
• Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, et al. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 37(8):852–16. doi: 10.1038/s41587-019-0209-9.
   PubMed Web of Science ®Google Scholar
• Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. 2016. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 13(7):581–583. doi: 10.1038/nmeth.3869.
   PubMed Web of Science ®Google Scholar
• Cheong CJ, Okada M. 2001. Effects of spilled oil on the tidal flat ecosystem–evaluation of wave and tidal actions using a tidal flat simulator. Water Sci Technol. 43(2):171–177. doi: 10.2166/wst.2001.0087.
   PubMed Web of Science ®Google Scholar
• Ding Y, Chen Y, Lin Z, Tuo Y, Li H, Wang Y. 2021. Differences in soil microbial community composition between suppressive and root rot-conducive in tobacco fields. Curr Microbiol. 78(2):624–633. doi: 10.1007/s00284-020-02318-3.
   PubMed Web of Science ®Google Scholar
• Ehlers BK, Berg MP, Staudt M, Holmstrup M, Glasius M, Ellers J, Tomiolo S, Madsen RB, Slotsbo S, Penuelas J, et al. 2020. Plant secondary compounds in soil and their role in belowground species interactions . Trends Ecol Evol. 35(8):716–730. doi: 10.1016/j.tree.2020.04.001.
   PubMed Web of Science ®Google Scholar
• Eisenhauer N, Scheu S, Jousset A. 2012. Bacterial diversity stabilizes community productivity . PLOS One. 7(3):e34517. doi: 10.1371/journal.pone.0034517.
   PubMed Web of Science ®Google Scholar
• Fan X, Zhang L, Yuan L, Guo B, Zhang Q, Wang Y, Wu Q. 2023. Loss of tidal creek ecosystem vitality caused by tidal flat narrowing on the central Jiangsu coast, China. Sci Total Environ. 864:161216. doi: 10.1016/j.scitotenv.2022.161216.
   PubMed Web of Science ®Google Scholar
• Fu L, Xie R, Ma D, Zhang M, Liu L. 2023. Variations in soil microbial community structure and extracellular enzymatic activities along a forest-wetland ecotone in high-latitude permafrost regions. Ecol Evol J. 13(6):e10205. doi: 10.1002/ece3.10205.
   PubMed Web of Science ®Google Scholar
• Furey GN, Tilman D. 2021. Plant biodiversity and the regeneration of soil fertility. Proc Natl Acad Sci U S A. 118(49):e2111321118. doi: 10.1073/pnas.2111321118.
   PubMed Web of Science ®Google Scholar
• Guo L, Tóth T, Yang F, Wang Z. 2023. Effects of different types of vegetation cover on soil microorganisms and humus characteristics of soda-saline land in the Songnen Plain. Front Microbiol. 14:1163444. doi: 10.3389/fmicb.2023.1163444.
   PubMed Web of Science ®Google Scholar
• Hill NK, Woodworth BK, Phinn SR, Murray NJ, Fuller RA. 2021. Global protected-area coverage and human pressure on tidal flats. Conserv Biol. 35(3):933–943. doi: 10.1111/cobi.13638.
   PubMed Web of Science ®Google Scholar
• Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM, et al. 2013. Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol. 22(21):5271–5277. doi: 10.1111/mec.12481.
   PubMed Web of Science ®Google Scholar
• Lan LY, Yang WQ, Wu FZ, Liu YW, Yang F, Guo CH, et al. 2019. Effects of soil fauna on microbial community during litter decomposition of Populus simonii and Fargesia spathacea in the subalpine forest of western Sichuan, China. . Ying Yong Sheng Tai Xue Bao. 30:2983–2991.
   PubMedGoogle Scholar
• Li F, Guo Y, Wang Z, Mu Y. 2022. Influence of different phytoremediation on soil microbial diversity and community composition in saline-alkaline land]. Int J Phytoremediation. 24(5):507–517. doi: 10.1080/15226514.2021.1955240.
   PubMed Web of Science ®Google Scholar
• Li HL, Ma B, Zhang XL, Zhang QQ, Guo XH, Fan P, et al. 2016. Diversity of culturable endophytic fungi of common reed (Phragmites australis) in coastal wetland. Ying Yong Sheng Tai Xue Bao. 27:2066–2074.
   PubMedGoogle Scholar
• Li J, Chen Q, Li Q, Zhao C, Feng Y. 2021. Influence of plants and environmental variables on the diversity of soil microbial communities in the Yellow River Delta Wetland, China. Chemosphere. 274:129967. doi: 10.1016/j.chemosphere.2021.129967.
   PubMed Web of Science ®Google Scholar
• Li PD, Jeewon R, Aruna B, Li HY, Lin FC, Wang HK. 2019. Metabarcoding reveals differences in fungal communities between unflooded versus tidal flat soil in coastal saline ecosystem. Sci Total Environ. 690:911–922. doi: 10.1016/j.scitotenv.2019.06.473.
   PubMed Web of Science ®Google Scholar
• Liang P, Jingan X, Liying S. 2022. The effects of reclaimed water irrigation on the soil characteristics and microbial populations of plant rhizosphere. Environ Sci Pollut Res Int. 29(12):17570–17579. doi: 10.1007/s11356-021-16983-9.
   PubMed Web of Science ®Google Scholar
• Martin M. 2011. CUTADAPT removes adapter sequences from high-throughput sequencing reads. EMBnet j. 17(1):10–12. doi: 10.14806/ej.17.1.200.
   Google Scholar
• Molnár Z, Solomon W, Mutum L, Janda T. 2023. Understanding the mechanisms of Fe deficiency in the rhizosphere to promote plant resilience. Plants . 12(10):1945. doi: 10.3390/plants12101945.
   Google Scholar
• Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41(Database issue):D590–6. doi: 10.1093/nar/gks1219.
   PubMed Web of Science ®Google Scholar
• Ravin NV, Mardanova AV, Skryabin KG. 2015. Metagenomics as a Tool for the Investigation of Uncultured Microorganisms. Genetika. 51:519–528.
   PubMedGoogle Scholar
• Sarkar S, Kamke A, Ward K, Hartung E, Ran Q, Feehan B, Galliart M, Jumpponen A, Johnson L, Lee STM, et al. 2022. Pseudomonas cultivated from Andropogon gerardii rhizosphere show functional potential for promoting plant host growth and drought resilience. BMC Genomics. 23(1):784. doi: 10.1186/s12864-022-09019-0.
   PubMed Web of Science ®Google Scholar
• Shao T, Gu X, Zhu T, Pan X, Zhu Y, Long X, Shao H, Liu M, Rengel Z. 2019. Industrial crop Jerusalem artichoke restored coastal saline soil quality by reducing salt and increasing diversity of bacterial community. Appl Soil Ecol. 138:195–206. doi: 10.1016/j.apsoil.2019.03.003.
   Web of Science ®Google Scholar
• Stevens H, Brinkhoff T, Rink B, Vollmers J, Simon M. 2007. Diversity and abundance of Gram positive bacteria in a tidal flat ecosystem . Environ Microbiol. 9(7):1810–1822. doi: 10.1111/j.1462-2920.2007.01302.x.
   PubMed Web of Science ®Google Scholar
• Tang Q, Li Q, Tong L, Wu R, Xu J. 2023. Rhizospheric soil organic carbon accumulated but its molecular groups redistributed via rhizospheric soil microorganisms along multi-root Cerasus humilis plantation chronosequence at the karst rocky desertification control area. Environ Sci Pollut Res Int. 30(28):72993–73007. doi: 10.1007/s11356-023-27588-9.
   PubMed Web of Science ®Google Scholar
• Tkacz A, Ledermann R, Martyn A, Schornack S, Oldroyd GED, Poole PS. 2022. Nodulation and nitrogen fixation in Medicago truncatula strongly alters the abundance of its root microbiota and subtly affects its structure. Environ Microbiol. 24(11):5524–5533. doi: 10.1111/1462-2920.16164.
   PubMed Web of Science ®Google Scholar
• Van Ryckegem G, Gessner MO, Verbeken A. 2007. Fungi on leaf blades of Phragmites australis in a brackish tidal marsh: diversity, succession, and leaf decomposition. Microb Ecol. 53(4):600–611. doi: 10.1007/s00248-006-9132-y.
   PubMed Web of Science ®Google Scholar
• Van Ryckegem G, Van Driessche G, Van Beeumen JJ, Verbeken A. 2006. The estimated impact of fungi on nutrient dynamics during decomposition of Phragmites australis leaf sheaths and stems. Microb Ecol. 52(3):564–574. doi: 10.1007/s00248-006-9003-6.
   PubMed Web of Science ®Google Scholar
• Walter J, Buchmann CM, Schurr FM. 2020. Shifts in plant functional community composition under hydrological stress strongly decelerate litter decomposition. Ecol Evol. 10(12):5712–5724. doi: 10.1002/ece3.6310.
   PubMed Web of Science ®Google Scholar
• Wang J, Wang Y, He N, Ye Z, Chen C, Zang R, Feng Y, Lu Q, Li J. 2020. Plant functional traits regulate soil bacterial diversity across temperate deserts. Sci Total Environ. 715:136976. doi: 10.1016/j.scitotenv.2020.136976.
   PubMed Web of Science ®Google Scholar
• Wang W, Wang Z, Yang K, Wang P, Wang H, Guo L, Zhu S, Zhu Y, He X. 2020. Biochar application alleviated negative plant-soil feedback by modifying soil microbiome. Front Microbiol. 11:799. doi: 10.3389/fmicb.2020.00799.
   PubMed Web of Science ®Google Scholar
• Yang Y, Liu H, Yang X, Yao H, Deng X, Wang Y, An S, Kuzyakov Y, Chang SX. 2022. Plant and soil elemental C: n: p ratios are linked to soil microbial diversity during grassland restoration on the Loess Plateau, China. Sci Total Environ. 806(Pt 1):150557. doi: 10.1016/j.scitotenv.2021.150557.
   PubMedGoogle Scholar
• Yu Y, Liu H, Zhang L, Sun Z, Lei B, Miao Y, Chu H, Han S, Shi Y, Zheng J, et al. 2023. Distinct response patterns of plants and soil microorganisms to agronomic practices and seasonal variation in a floodplain ecosystem. Front Microbiol. 14:1094750. doi: 10.3389/fmicb.2023.1094750.
   PubMed Web of Science ®Google Scholar
• Zhang ZF, Yu QG, Wang H, Liu HH, Zhao YC, Xie XY. 2021.Effects of plant community and soil properties on soil bacterial community in Bitahai Wetland, Southwest China]. Ying Yong Sheng Tai Xue Bao. 32:2199–2208.
   PubMedGoogle Scholar
• Zhao Y, Liu Q, Huang R, Pan H, Xu M. 2020. Recent evolution of Coastal Tidal flats and the impacts of intensified human activities in the Modern Radial Sand Ridges, East China. Int J Environ Res Public Health. 17(9):3191. doi: 10.3390/ijerph17093191.
   Web of Science ®Google Scholar