Meta-Analysis of Organic Fertilization Effects on Soil Bacterial Diversity and Community Composition in Agroecosystems
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ABSTRACT:
SUBMITTER: Shu X
PROVIDER: S-EPMC10675672 | biostudies-literature | 2023 Nov
REPOSITORIES: biostudies-literature
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Project description:Shifts in soil bacterial diversity and community composition are suggested to be induced by elevated input of nitrogen (N) fertilization with implications for soil quality, and consequently production. In this study, we evaluated the impacts of recommended fertilization (RF) and conventional fertilization (CF) on soil chemical properties, crop yield, bacterial diversity, and community composition from two long-term experiments conducted in fluvo-aquic soil and black soil of China. Each site comprised of four treatments, i.e., RF N-, RF N+, CF N-, CF N+. No N fertilization was indicated by N- and N fertilization was indicated by N+. Across both sites, N fertilization significantly increased crop yield compared with no N fertilization and RF successfully enhanced crop yield over CF. Interestingly, the RF maintained bacterial diversity, while CF depressed bacterial diversity in the two soils. Microbial taxa performing important ecological roles such as order Rhodospirillales and Bacillales were significantly enhanced in the RF approach, while Rhizobiales declined under CF. Furthermore, the results of partial least square path modeling revealed that soil available phosphorus (AP) negatively affected bacterial diversity while it positively affected bacterial community structure in fluvo-aquic soils. In contrast, soil pH was positively linked with both bacterial diversity and community structure in black soil. Overall, our study demonstrated that RF is an environmentally friendly approach which not only maintained above ground plant productivity, but also preserved belowground microbial populations and important soil variables regulating bacterial communities varied in different soil types.
| S-EPMC7466009 | biostudies-literature
Project description:This study investigated the effects of long-term soil fertilization on the composition and potential for phosphorus (P) and nitrogen (N) cycling of bacterial communities associated with hyphae of the P-solubilizing fungus Penicillium canescens Using a baiting approach, hyphosphere bacterial communities were recovered from three soils that had received long-term amendment in the field with mineral or mineral plus organic fertilizers. P. canescens hyphae recruited bacterial communities with a decreased diversity and an increased abundance of Proteobacteria relative to what was observed in soil communities. As core bacterial taxa, Delftia and Pseudomonas spp. were present in all hyphosphere samples irrespective of soil fertilization. However, the type of fertilization showed significant impacts on the diversity, composition, and distinctive taxa/operational taxonomic units (OTUs) of hyphosphere communities. The soil factors P (Olsen method), exchangeable Mg, exchangeable K, and pH were important for shaping soil and hyphosphere bacterial community compositions. An increased relative abundance of organic P metabolism genes was found in hyphosphere communities from soil that had not received P fertilizers, which could indicate P limitation near the fungal hyphae. Additionally, P. canescens hyphae recruited bacterial communities with a higher abundance of N fixation genes than found in soil communities, which might imply a role of hyphosphere communities for fungal N nutrition. Furthermore, the relative abundances of denitrification genes were greater in several hyphosphere communities, indicating an at least partly anoxic microenvironment with a high carbon-to-N ratio around the hyphae. In conclusion, soil fertilization legacy shapes P. canescens hyphosphere microbiomes and their functional potential related to P and N cycling.IMPORTANCE P-solubilizing Penicillium strains are introduced as biofertilizers to agricultural soils to improve plant P nutrition. Currently, little is known about the ecology of these biofertilizers, including their interactions with other soil microorganisms. This study shows that communities dominated by Betaproteobacteria and Gammaproteobacteria colonize P. canescens hyphae in soil and that the compositions of these communities depend on the soil conditions. The potential of these communities for N and organic P cycling is generally higher than that of soil communities. The high potential for organic P metabolism might complement the ability of the fungus to solubilize inorganic P, and it points to the hyphosphere as a hot spot for P metabolism. Furthermore, the high potential for N fixation could indicate that P. canescens recruits bacteria that are able to improve its N nutrition. Hence, this community study identifies functional groups relevant for the future optimization of next-generation biofertilizer consortia for applications in soil.
| S-EPMC7205497 | biostudies-literature
Project description:Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community at the functional gene level to long-term fertilization, especially integrated fertilization (chemical combined with organic fertilization) remain unclear. Here we used microarray-based GeoChip techniques to explore the shifts of soil microbial functional community in a nutrient-poor paddy soil with long-term (21 years).The long-term fertilization experiment site (set up in 1990) was located in Taoyuan agro-ecosystem research station (28°55’N, 111°27’E), Chinese Academy of Sciences, Hunan Province, China, with a double-cropped rice system. fertilization at various regimes.
2020-09-19 | GSE104014 | GEO
Project description:Pastures are an important part of crop and food systems in cold climates. Understanding how fertilization and plant species affect soil bacterial community diversity and composition is the key for understanding the role of soil bacteria in sustainable agriculture. To study the response of soil bacteria to different fertilization and cropping managements, a 3-year (2013-2015) field study was established. In the split-plot design, fertilizer treatment (unfertilized control, organic fertilizer, and synthetic fertilizer) was the main plot factor, and plant treatment [clear fallow, red clover (Trifolium pratense), timothy (Phleum pratense), and a mixture of red clover and timothy] was the sub-plot factor. Soil bacterial community diversity and composition, soil properties, and crop growth were investigated through two growing seasons in 2014 and 2015, with different nitrogen input levels. The community diversity measures (richness, Shannon diversity, and Shannon evenness) and composition changed over time (P < 0.05) and at different time scales. The community diversity was lower in 2014 than in 2015. The temporal differences were greater than the differences between treatments. The overall correlations of Shannon diversity to soil pH, NO 3 - , NH 4 + , and surplus nitrogen were positive and that of bacterial richness to crop dry matter yield was negative (P < 0.05). The major differences in diversity and community composition were found between fallow and planted treatments and between organic and synthetic fertilizer treatments. The differences between the planted plots were restricted to individual operational taxonomic units (OTUs). Soil moisture, total carbon content, and total nitrogen content correlated consistently with the community composition (P < 0.05). Compared to the unfertilized control, the nitrogen fertilizer loading enhanced the temporal change of community composition in pure timothy and in the mixture more than that in red clover, which further emphasizes the complexity of interactions between fertilization and cropping treatments on soil bacteria.
| S-EPMC7419661 | biostudies-literature
Project description:IntroductionA better understanding of the regulatory role of microorganisms on soil phosphorous (P) mobilization is critical for developing sustainable fertilization practices and reducing P resource scarcity. The phoD genes regulate soil organic P (Po) mobilization.MethodsBased on the long-term P application experiments in acid purple soil of maize system in Southwest China (started in 2010), the experiment included five P levels: 0, 16, 33, 49, and 65.5 kg P hm-2 (P0, P16, P33, P49, and P65.5, respectively). The molecular speciation of organic P in soil was determined by 31P-nuclear magnetic resonance (NMR), high-throughput sequencing technology, and real-time qPCR were used to analyze the bacterial community and abundance of phoD-harboring bacterial genes, exploring the bacterial community and abundance characteristics of phoD gene and its relationship with the forms of Po and alkaline phosphatase (ALP) activity in the soil.ResultsThe results showed that the orthophosphate monoesters (OM) were the main Po speciation and varied by P fertilization in acid purple soil. ALP activity decreased as P fertilization increased. Co-occurrence network analysis identified the overall network under five P fertilizations. The keystone taxon base on the network showed that Collimonas, Roseateles, Mesorhizobium, and Cellulomonas positively correlated with both OM and Po. The random forest showed that Cellulomonas, Roseateles, and Rhodoplanes were the key predictors for ALP activity. The keystone taxon was a more important predictor than the dominant taxon for ALP, OM, and Po. The structural equation model (SEM) showed that soil organic matter (SOM), available P (AP), and OM were the main factors influencing the ALP by reshaping phoD-harboring bacteria alpha diversity, community composition, and phoD abundance.DiscussionThe phoD-harboring bacterial community composition especially the keystone taxon rather than alpha diversity and abundance dominated the ALP activity, which could promote P utilization over an intensive agroecosystem. These findings improve the understanding of how long-term gradient fertilization influences the community composition and function of P-solubilizing microorganisms in acid purple soil.
| S-EPMC9730253 | biostudies-literature
Project description:The application of pesticides may have significant impacts on soil environment and communities. In order to understand the deep relationship between the application of chlormequat chloride (CC) and the bacterial community in peanut soil, high-resolution characterization was performed using peanut soil samples (12 points; 0-20 cm rhizosphere soil) from untreated and sprayed with different concentrations of CC. Experimental data showed that with the increase of concentration, operational taxonomic units (OTUs) richness showed a decreasing tendency. The OTUs richness at low concentration (D, 50% CC diluted 5000 times, 45 g ai/ha), medium concentration (M, 50% CC diluted 300 times, 75 g ai/ha), and high concentration (G, 50% CC diluted 1000 times, 225 g ai/ha) were 5583, 5430, and 3910, respectively. Low concentrations increased the composition and relative abundance of soil bacterial communities. In contrast, high concentrations significantly reduced bacterial diversity. As the concentration of CC increases, the abundance of Proteobacteria decreases, while the abundance of Firmicutes and Bacteroidetes increases. The number of Acidobacterium and Bacteroidetes increased in groups D and M, while it decreased in group G. D, M and G groups showed a decrease in the abundance of Pseudomonas, polaromonas, and Azovibrio compared to CK, while the abundance of Flavobacterium increased. In addition, the abundance of Rahnella1 decreased in groups D and M, while the abundance increased in group G. The main metabolic pathways included the metabolisms of nucleotides, terpenoids, polyketides, other amino acids, cofactors, vitamins, lipids, glycan biosynthesis, energy, carbohydrates, xenobiotics, amino acids, and other secondary metabolites.
| S-EPMC11895187 | biostudies-literature
Project description:The aim of this study was to assess the effects of irrigation frequency and nitrogen fertilization rate on the abundance, diversity, and composition of soil bacteria in winter wheat. Irrigation, but not nitrogen fertilization, significantly affected the bacterial alpha diversity index. Among the 50 phyla obtained in these treatments, Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria, Gemmatimonadetes, and Firmicutes were the predominant phyla. The LEfSe analysis of different treatments indicated that irrigation had a stronger effect on soil bacteria community composition than nitrogen fertilization. Moreover, the soil pH, moisture, available phosphorus (AP), and available potassium (AK) significantly correlated with the relative abundance of dominant bacteria at the phylum, genus, and operational taxonomic unit (OTU) levels. Overall, after three years of irrigation and fertilization treatments, the effect of irrigation on soil bacteria abundance, diversity, and composition of winter wheat was stronger than that of nitrogen fertilization, highlighting the importance of water availability for bacteria communities in semi-arid ecosystems. Inorganic and organic fertilizers should be applied in rotation.
| S-EPMC8377015 | biostudies-literature
Project description:Soil microorganisms play a pivotal role in carbon mineralization and their diversity is crucial to the function of soil ecosystems. However, the effects of long-term fertilization on microbial-mediated carbon mineralization are poorly understood. To identify the relative roles of microbes in carbon mineralization of yellow paddies, we investigated the long-term fertilization effects on soil properties and microbial communities and their relationships with carbon mineralization. The treatments included: no fertilization (CK), chemical fertilizer (NPK), organic fertilizer (M), and constant organic-inorganic fertilizer (MNPK). NPK treatment significantly increased soil water content (WC), while M and MNPK treatments significantly increased the content of soil organic carbon (SOC), total nitrogen (TN), soil microbial biomass carbon (SMBC), soil microbial biomass nitrogen (SMBN), and WC. Strong increases in CO2 emissions, potential mineralized carbon, and turnover rate constant were observed in both organic-fertilizer treatments (M and MNPK), relative to the CK treatment. These changes in soil properties can be attributed to the variation in microbial communities. NPK treatment had no significant effect. Different fertilization treatments changed soil microbial community; SOC and SMBN were the most important contributors to the variance in microbial community composition. The variations in community composition did not significant influence carbon mineralization; however, carbon mineralization was significantly influenced by the abundance of several non-dominant bacteria. The results suggest that SOC, SMBN, and non-dominant bacteria (Gemmatimonadetes and Latescibacteria), have a close relationship to carbon mineralization, and should be preferentially considered in predicting carbon mineralization under long-term fertilization.
| S-EPMC6347141 | biostudies-literature
Project description:A strategic selection of tree species will shift the type and quality of litter input, and subsequently magnitude and composition of the soil organic carbon (SOC) through soil microbial community. We conducted a manipulative experiment in randomized block design with leaf litter inputs of four native subtropical tree species in a Pinus massoniana plantation in southern China and found that the chemical composition of SOC did not differ significantly among treatments until after 28 months of the experiment. Contrasting leaf litter inputs had significant impacts on the amounts of total microbial, Gram-positive bacterial, and actinomycic PLFAs, but not on the amounts of total bacterial, Gram-negative bacterial, and fungal PLFAs. There were significant differences in alkyl/O-alkyl C in soils among the leaf litter input treatments, but no apparent differences in the proportions of chemical compositions (alkyl, O-alkyl, aromatic, and carbonyl C) in SOC. Soil alkyl/O-alkyl C was significantly related to the amounts of total microbial, and Gram-positive bacterial PLFAs, but not to the chemical compositions of leaf litter. Our findings suggest that changes in forest leaf litter inputs could result in changes in chemical stability of SOC through the altered microbial community composition.
| S-EPMC4891773 | biostudies-other
Project description:It is generally assumed that the dependence of conventional agriculture on artificial fertilizers and pesticides strongly impacts the environment, while organic agriculture relying more on microbial functioning may mitigate these impacts. However, it is not well known how microbial diversity and community composition change in conventionally managed farmers' fields that are converted to organic management. Here, we sequenced bacterial and fungal communities of 34 organic fields on sand and marine clay soils in a time series (chronosequence) covering 25 years of conversion. Nearby conventional fields were used as references. We found that community composition of bacteria and fungi differed between organic and conventionally managed fields. In the organic fields, fungal diversity increased with time since conversion. However, this effect disappeared when the conventional paired fields were included. There was a relationship between pH and soil organic matter content and the diversity and community composition of bacteria and fungi. In marine clay soils, when time since organic management increased, fungal communities in organic fields became more dissimilar to those in conventional fields. We conclude that conversion to organic management in these Dutch farmers' fields did not increase microbial community diversity. Instead, we observed that in organic fields in marine clay when time since conversion increased soil fungal community composition became progressively dissimilar from that in conventional fields. Our results also showed that the paired sampling approach of organic and conventional fields was essential in order to control for environmental variation that was otherwise unaccounted for.
| S-EPMC9545909 | biostudies-literature