Bio-organic fertilizers improve Dendrocalamus farinosus growth by remolding the soil microbiome and metabolome

Abstract

Organic and microbial fertilizers have potential advantages over inorganic fertilizers in improving soil fertility and crop yield without harmful side-effects. However, the effects of these bio-organic fertilizers on the soil microbiome and metabolome remain largely unknown, especially in the context of bamboo cultivation. In this study, we cultivated Dendrocalamus farinosus (D. farinosus) plants under five different fertilization conditions: organic fertilizer (OF), Bacillus amyloliquefaciens bio-fertilizer (Ba), Bacillus mucilaginosus Krassilnikov bio-fertilizer (BmK), organic fertilizer plus Bacillus amyloliquefaciens bio-fertilizer (OFBa), and organic fertilizer plus Bacillus mucilaginosus Krassilnikov bio-fertilizer (OFBmK). We conducted 16S rRNA sequencing and liquid chromatography/mass spectrometry (LC–MS) to evaluate the soil bacterial composition and soil metabolic activity in the different treatment groups. The results demonstrate that all the fertilization conditions altered the soil bacterial community composition. Moreover, the combination of organic and microbial fertilizers (i.e., in the OFBa and OFBmK groups) significantly affected the relative abundance of soil bacterial species; the largest number of dominant microbial communities were found in the OFBa group, which were strongly correlated with each other. Additionally, non-targeted metabolomics revealed that the levels of soil lipids and lipid-like molecules, and organic acids and their derivatives, were greatly altered under all treatment conditions. The levels of galactitol, guanine, and deoxycytidine were also markedly decreased in the OFBa and OFBmK groups. Moreover, we constructed a regulatory network to delineated the relationships between bamboo phenotype, soil enzymatic activity, soil differential metabolites, and dominant microbial. The network revealed that bio-organic fertilizers promoted bamboo growth by modifying the soil microbiome and metabolome. Accordingly, we concluded that the use of organic fertilizers, microbial fertilizers, or their combination regulated bacterial composition and soil metabolic processes. These findings provide new insights into how D. farinosus-bacterial interactions are affected by different fertilization regiments, which are directly applicable to the agricultural cultivation of bamboo.

Long-term effects of farmyard manure addition on soil organic matter molecular composition: C transformation as a major driver of energetic potential

“…This parallels with earlier reports of shifts in SOM composition due to long-term FYM addition, including higher molecular weight and carboxyl contents (Ellerbrock et al, 1999). Multiple studies reported increased abundances of non-polar, aliphatic, oxidized an N-containing compounds (most likely fatty acids, and amino acids) (Gerzabek et al, 2006;Ye et al, 2019;Shi et al, 2022;Li et al, 2023;Tang et al, 2023) and decreased abundances of phenolics or aromatic signals upon continued manure addition (Mao et al, 2008;Shi et al, 2022;Tang et al, 2023). We did not find elevated N in markers related to Cat.…”

“…Accumulation of SOC upon OM inputs, including FYM, have been accurately modelled using one parameter (h for "humification", linked to the fraction of remaining C) but the molecular mechanisms behind that parameter are poorly understood (Levavasseur et al, 2020). Molecular-level analyses using a wide range of methods have reported increases in aliphaticity, carboxyl-C, peptides, lipids and lipidlike molecules, oxygen-enriched compounds, nonpolar alkyl compounds (likely fatty acids), alkyl C, alkyl-O C and di-O-alkyl C over a simultaneous decrease in phenolics and aromatic C as compared to control treatments (Ellerbrock et al, 1999;Gerzabek et al, 2006;Mao et al, 2008;Ye et al, 2019;Shi et al, 2022;Li et al, 2023;Tang et al, 2023). In contrast, some studies have reported an increase of aromatic structures or lignin, and recalcitrance upon receiving organic amendments (Leifeld et al, 2002;Peltre et al, 2017;Ye et al, 2019).…”

“…) or individual biomarker level (lignin phenols, amino sugars, etc.). Few have employed non-targeted metabolomics approaches having the potential to elucidating SOM formation, turnover, and stabilization on a molecular level (Li et al, 2023;Brown et al, 2024;Song et al, 2024). Tang et al (2023) used liquid chromatography coupled to time of flight tandem mass spectrometry (LC-MS) and found that extractable SOM (using organic solvents) responded to long-term FYM addition.…”

Sustainable Use of Organic Seaweed Fertilizer Improves the Metagenomic Function of Microbial Communities in the Soil of Rice Plants

“…Notably, there is a large portion of the Archaea phylum Crenarchaeota in the CFSF2 group. The phylum Crenarchaeota is most commonly abundant in marine environments [52]. However, there are some novel Crenarchaeota found in forest and also paddy soil [53,54].…”

Evaluating the impact of various biofertilizer sources on growth and yield attributes of spring rice (Oryza sativa L.) in Eastern Terai of Nepal

“…The use of biofertilizer, which contains helpful microorganisms, helps to slow down the breakdown of organic matter and improve the availability of vital plant nutrients, including nitrogen, phosphorous, sulfur and phosphorous (Jena et al, 2020). As a result, the presence of beneficial microbes in biofertilizers increases soil water retention, stimulates soil aggregate growth (Li et al, 2023), and has a buffering impact on soil acidity, alkalinity, salinity, harmful heavy metals, and, pesticides (Yengkokpam et al, 2022). Furthermore, biofertilizer could reduce the cost of production, and eco-friendly, and renewable sources of plant nutrients (Sarker et al, 2018).…”