Manure amendment and the rhizosphere of Amaranthus hybridus soil bacterial communities in a semi-arid irrigated agroecosystem
DOI:
https://doi.org/10.19136/era.a13nVI.5239Keywords:
16s rRNA, soil bacterial diversity, soil ecological engineeringAbstract
Soil biodiversity is fundamental to nutrient cycling and ecosystem functioning in agroecosystems, yet the combined effects of organic amendments and weed rhizospheres on soil bacterial communities remain insufficiently explored in semi-arid irrigated systems. We evaluated soil physicochemical properties and bacterial diversity inferred from 16S rRNA gene amplicon sequencing in three soil treatments: initial bulk soil (T1), bulk soil amended with cattle manure at 20 Mg ha-1 and sampled 11 days after application (T2), and the rhizosphere of Amaranthus hybridus sampled 75 days after manure application (T3). Alpha diversity (Faith's phylogenetic diversity, Shannon diversity, and evenness), beta diversity (Bray–Curtis, weighted UniFrac, and unweighted UniFrac), PERMANOVA, and redundancy analysis (RDA) were used to characterize bacterial communities. Manure amendment increased bacterial richness and alpha diversity, whereas the A. hybridus rhizosphere exhibited intermediate diversity, a distinct taxonomic composition, and higher micronutrient concentrations. Multivariate analyses further demonstrated clear differences in bacterial community composition among treatments and strong associations between dominant bacterial taxa and soil physicochemical gradients. These findings indicate that manure amendment and rhizosphere-associated processes jointly promote heterogeneous bacterial community configurations in semi-arid irrigated agroecosystems.
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Berendsen RL, Pieterse CMJ, Bakker PAHM (2012) The rhizosphere microbiome and plant health. Trends in Plant Science 17: 478-486. https://doi.org/10.1016/j.tplants.2012.04.001
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Caporaso JG (2019) Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology 37(8): 852-857. https://doi.org/10.1038/s41587-019-0209-9
Bulgarelli D, Schlaeppi K, Spaepen S, Van Themaat EVL, Schulze-Lefert P (2013) Structure and functions of the bacterial microbiota of plants. Annual Review of Plant Biology 64: 807-838. https://doi.org/10.1146/annurev-arplant-050312-120106
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP (2016) DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods 13(7): 581-583. https://doi.org/10.1038/nmeth.3869
Chen J, Zhang Y, Kuzyakov Y, Wang D, Olesen JE (2023) Challenges in upscaling laboratory studies to ecosystems in soil microbiology research. Global Change Biology 29(3): 569-574. https://doi.org/10.1111/gcb.16537
Delgado-Baquerizo M, Eldridge D, Ochoa V, Gozalo B, Singh B, Maestre F (2017) Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe. Ecology Letters 20: 1295-1305. https://doi.org/10.1111/ele.12826
Delgado-Baquerizo M, Maestre FT, Reich PB, Jeffries TC, Gaitan JJ, Encinar D, Berdugo M, Campbell CD, Singh BK (2016) Microbial diversity drives multifunctionality in terrestrial ecosystems. Nature Communications 7: 10541. https://doi.org/10.1038/ncomms10541
Fernández-Huarte M, Elphinstone JG, Adams IP, Vicente JG, Bhogal A, Watson CA, Dussart F, Stockdale EA, Walshaw J, McGreig S, Simmons RW, Mašková L, Deeks LK, Goddard MR (2023) A DNA-barcode biodiversity standard analysis method (DNA-BSAM) reveals a large variance in the effect of a range of biological, chemical and physical soil management interventions at different sites, but location is one of the most important aspects determining the nature of agricultural soil microbiology. Soil Biology and Biochemistry 184: 109104. https://doi.org/10.1016/j.soilbio.2023.109104
Fierer N (2017) Embracing the unknown: Disentangling the complexities of the soil microbiome. Nature Reviews Microbiology 15(10): 579-590. https://doi.org/10.1038/nrmicro.2017.87
Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88(6): 1354-1364. https://doi.org/10.1890/05-1839
Hartmann M, Frey B, Mayer J, Mäder P, Widmer F (2015) Distinct soil microbial diversity under long-term organic and conventional farming. The ISME Journal 9(5): 1177-1194. https://doi.org/10.1038/ismej.2014.210
Ke J, Wang B, Yoshikuni Y (2021) Microbiome engineering: Synthetic biology of plant-associated microbiomes in sustainable agriculture. Trends in Biotechnology 39(3): 244-261. https://doi.org/10.1016/j.tibtech.2020.07.008
Kushwaha P, Soto-Velázquez AL, McMahan C, Neilson JW (2024) Field to greenhouse: how stable is the soil microbiome after removal from the field? Microorganisms 12(1): 110 https://doi.org/10.3390/microorganisms12010110
Li Q, Guo J, Zhang H, Zhao M (2024) The competition between Bidens pilosa and Setaria viridis alters soil microbial composition and soil ecological function. Journal of Integrative Agriculture 23(1): 267-282. https://doi.org/10.1016/j.jia.2023.07.025
Liu J, Shu A, Song W, Shi W, Li M, Zhang W, Li Z, Liu G, Yuan F, Zhang S, Liu Z, Gao Z (2021) Long-term organic fertilizer substitution increases rice yield by improving soil properties and regulating soil bacteria. Geoderma 404: 115287. https://doi.org/10.1016/j.geoderma.2021.115287
Luján-Soto R, Martínez-Mena M, Cuéllar-Padilla M, De-Vente J (2021) Restoring soil quality of woody agroecosystems in Mediterranean drylands through regenerative agriculture. Agriculture, Ecosystems & Environment 306: 107191. https://doi.org/10.1016/j.agee.2020.107191
Lupatini M, Korthals GW, de Hollander M, Janssens TKS, Kuramae EE (2017) Soil microbiome is more heterogeneous in organic than in conventional farming system. Frontiers in Microbiology 7: 2064. https://doi.org/10.3389/fmicb.2016.02064
McDonald D, Jiang Y, Balaban M, Cantrell K, Zhu Q, Gonzalez A, Morton J T, Nicolaou G, Parks D H, Karst S M, Albertsen M, Hugenholtz P, DeSantis T, Song S J, Bartko A, Havulinna A S, Jousilahti P, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Lahti L, Mirarab S, Knight R (2024) Greengenes2 unifies microbial data in a single reference tree. Nature Biotechnology 42: 715-718
Meena VS, Meena SK, Verma JP, Kumar A, Aeron A, Mishra PK, Bisht JK, Pattanayak A, Naveed M, Dotaniya ML (2017) Plant beneficial rhizospheric microorganism (PBRM) strategies to improve nutrient use efficiency: A review. Ecological Engineering 107: 8-32. https://doi.org/10.1016/j.ecoleng.2017.06.058
Metsalu T, Vilo J (2015) Clustvis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and a heatmap. Nucleic Acids Research 43(W1): W566-W570. https://doi.org/10.1093/nar/gkv468
Montemayor-Trejo JA, Lara-Míreles JL, Woo-Reza JL, Munguía-López J, Rivera-González M, Trucíos-Caciano R (2012) Producción de maíz forrajero (Zea mays L.) en tres sistemas de irrigación en la Comarca Lagunera de Coahuila y Durango, México. Agrociencia 46(3): 267-278.
Ofek-Lalzar M, Sela N, Goldman-Voronov M, Green SJ, Hadar Y, Minz D (2014) Niche and host-associated functional signatures of the root surface microbiome. Nature Communications 5(1): 4950. https://doi.org/10.1038/ncomms5950
Peng M, Tabashsum Z, Millner P, Parveen S, Biswas D (2021) Influence of manure application on the soil bacterial microbiome in integrated crop–livestock farms in Maryland. Microorganisms 9(12): 2586. https://doi.org/10.3390/microorganisms9122586
Schmidt JE, Kent AD, Brisson VL, Gaudin ACM (2019) Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling. Microbiome 7(1): 146. https://doi.org/10.1186/s40168-019-0756-9
Sun Y, Snow D, Walia H, Li X (2021) Transmission routes of the microbiome and resistome from manure to soil and lettuce. Environmental Science & Technology 55(16): 11102-11112. https://doi.org/10.1021/acs.est.1c02985
Trivedi P, Leach JE, Tringe SG, Sa T, Singh BK (2020) Plant–microbiome interactions: From community assembly to plant health. Nature Reviews Microbiology 18: 607-621. https://doi.org/10.1038/s41579-020-0412-1
Tsiafouli MA, Thébault E, Sgardelis SP, de Ruiter PC, van der Putten WH, Birkhofer K, Hemerik L, de Vries FT, Bardgett RD, Brady MV, Bjornlund L, Jørgensen HB, Christensen S, Hertefeldt TD, Hotes S, Gera Hol WH, Frouz J, Liiri M, Mortimer SR, Hedlund K (2015) Intensive agriculture reduces soil biodiversity across Europe. Global Change Biology 21(2): 973-985. https://doi.org/10.1111/gcb.12752
Walkley A, Black IA (1934) An examination of the Degtjareff method for determining soil organic matter, and a proposed modification of the chromic acid titration method. Soil Science 37(1): 29-38.
Zegeye EK, Brislawn CJ, Farris Y, Fansler SJ, Hofmockel KS, Jansson JK, Wright AT, Graham EB, Naylor D, McClure RS, Bernstein HC (2019) Selection, succession, and stabilization of soil microbial consortia. mSystems 4(4): e00055-19. https://doi.org/10.1128/msystems.00055-19
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