Short-term effects of organic and inorganic fertilizers on soil microbial community structure and function
TL;DR: In this article, a field study was carried out to analyze the short-term impacts of replacing mineral by organic fertilizers on the microbial and biochemical parameters relevant for soil fertility and crop yield.
Abstract: A field study was carried out to analyze the short-term impacts of replacing mineral by organic fertilizers on the microbial and biochemical parameters relevant for soil fertility and crop yield. Three types of fertilization regimes were compared: (1) conventional fertilizer regime with inorganic fertilizer, and combined integrated fertilizer regimes in which 25 % of the nutrients were supplied by either (2) rabbit manure or (3) vermicompost. The effects on microbial community structure and function (phospholipid fatty acid [PLFA] profiles, bacterial growth, fungal growth, basal respiration, β-glucosidase, protease and phosphomonoesterase activities), soil biochemical properties (total C, dissolved organic carbon [DOC], N-NH4
+, N-NO3
−, PO4, total K) and crop yield were investigated in the samples collected from the experimental soil at harvest, 3 months after addition of fertilizer. The integrated fertilizer regimes stimulated microbial growth, altered the structure of soil microbial community and increased enzyme activity relative to inorganic fertilization. Bacterial growth was particularly influenced by the type of fertilizer regime supplied, while fungal growth only responded to the amount of fertilizer provided. The use of manure produced a fast increase in the abundance of PLFA biomarkers for Gram-negative bacteria as compared to inorganic fertilizer. Nutrient supply and crop yield with organic fertilizers were maintained at similar levels to those obtained with inorganic fertilizer. The effects of the organic amendments were observed even when they involved a small portion of the total amount of nutrients supplied; thereby confirming that some of the beneficial effects of integrated fertilizer strategies may occur in the short term.
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TL;DR: The data implicate the role of livestock manures in preventing the loss of bacterial diversity during long-term chemical fertilization, and highlight pH as the major deterministic factor for soil bacterial community structure.
Abstract: Addition of organic matter such as livestock manures and plant residues is a feasible practice to mitigate soil degradation caused by long-term application of chemical fertilizers, and the mitigation is largely mediated though activities of the soil-dwelling microorganisms. However, the roles of different kinds of organic matter in maintaining bacterial community structure have not been assessed in a comparative manner. In this study, 454 pyrosequencing of 16S rRNA gene was employed to compare the bacterial community structure among soils that had been subjected to 30 years of NPK fertilization under six treatment regimes: non-fertilization control, fertilization only, and fertilization combined with the use of pig manure, cow manure or low- and high-level of wheat straws. Consistent with expectation, long-term application of NPK chemical fertilizers caused a significant decrease of bacterial diversity in terms of species richness (i.e. number of unique operational taxonomic units (OTU)), Faith's index of phylogenetic diversity and Chao 1 index. Incorporation of wheat straw into soil produced little effects on bacterial community, whereas addition of either pig manure or cow manure restored bacterial diversity to levels that are comparable to that of the non-fertilization control. Moreover, bacterial abundance determined by quantitative PCR was positively correlated with the nutritional status of the soil (e.g., nitrate, total nitrogen, total carbon, available phosphorus); however, bacterial diversity was predominantly determined by soil pH. Together, our data implicate the role of livestock manures in preventing the loss of bacterial diversity during long-term chemical fertilization, and highlight pH as the major deterministic factor for soil bacterial community structure.
504 citations
TL;DR: The effects of different fertilization regimes (mineral, organic and combined mineral and organic fertilization), carried out for more than a century, on the structure and activity of the soil microbiome are reported.
Abstract: Soil management is fundamental to all agricultural systems and fertilization practices have contributed substantially to the impressive increases in food production. Despite the pivotal role of soil microorganisms in agro-ecosystems, we still have a limited understanding of the complex response of the soil microbiota to organic and mineral fertilization in the very long-term. Here we report the effects of different fertilization regimes (mineral, organic and combined mineral and organic fertilization), carried out for more than a century, on the structure and activity of the soil microbiome. Organic matter content, nutrient concentrations and microbial biomass carbon were significantly increased by mineral, and even more strongly by organic fertilization. Pyrosequencing revealed significant differences between the structures of bacterial and fungal soil communities associated to each fertilization regime. Organic fertilization increased bacterial diversity, and stimulated microbial groups (Firmicutes, Proteobacteria and Zygomycota) that are known to prefer nutrient-rich environments, and that are involved in the degradation of complex organic compounds. In contrast, soils not receiving manure harbored distinct microbial communities enriched in oligotrophic organisms adapted to nutrient-limited environments, as Acidobacteria. The fertilization regime also affected the relative abundances of plant beneficial and detrimental microbial taxa, which may influence productivity and stability of the agroecosystem. As expected, the activity of microbial exoenzymes involved in carbon, nitrogen and phosphorous mineralization were enhanced by both types of fertilization. However, in contrast to comparable studies, the highest chitinase and phosphatase activities were observed in the solely mineral fertilized soil. Interestingly, these two enzymes showed also a particular high biomass-specific activities and a strong negative relation with soil pH. As many soil parameters are known to change slowly, the particularity of unchanged fertilization treatments since 1902 allows a profound assessment of linkages between management and abiotic as well as biotic soil parameters. Our study revealed that pH and TOC were the majors, while nitrogen and phosphorous pools were minors, drivers for structure and activity of the soil microbial community. Due to the long-term treatments studied, our findings likely represent permanent and stable, rather than transient, responses of soil microbial communities to fertilization.
430 citations
Cites background or result from "Short-term effects of organic and i..."
...…the world, reporting that in most of the studies mineral fertilization led to a significant increase in the soil microbial biomass, while other field studies based on short-term application of N amendments found opposite results (Lupwayi et al., 2011; Roberts et al., 2011; Lazcano et al., 2013)....
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...…correlated with MBC, and a positive effect on microbial biomass by organic inputs has been well documented in long(Murugan and Kumar, 2013; Stagnari et al., 2014; Frossard et al., 2016) and short-term (Lagomarsino et al., 2009; Lazcano et al., 2013; Ma et al., 2016) agricultural studies....
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...Enhanced microbial activity as a consequence of organic manure applications have already been reported in short- (Dinesh et al., 2010; Lazcano et al., 2013) and long-term experiment (Giacometti et al., 2014; Zhang et al., 2015)....
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TL;DR: Deep 16S amplicon sequencing is used to investigate bacterial community characteristics in a fluvo-aquic soil treated for 24 years with inorganic fertilizers and organics and provides certain theoretical support for selection of rational fertilization strategies.
Abstract: Fertilization has a large impact on the soil microbial communities, which play pivotal roles in soil biogeochemical cycling and ecological processes. While the effects of changes in nutrient availability due to fertilization on the soil microbial communities have received considerable attention, specific microbial taxa strongly influenced by long-term organic and inorganic fertilization, their potential effects and associations with soil nutrients remain unclear. Here we use deep 16S amplicon sequencing to investigate bacterial community characteristics in a fluvo-aquic soil treated for 24 years with inorganic fertilizers and organics (manure and straw)-inorganic fertilizers, and uncover potential links between soil nutrient parameters and specific bacterial taxa. Our results showed that combined organic-inorganic fertilization increased soil organic carbon (SOC) and total nitrogen (TN) contents and altered bacterial community composition, while inorganic fertilization had little impact on soil nutrients and bacterial community composition. SOC and TN emerged as the major determinants of community composition. The abundances of specific taxa, especially Arenimonas, Gemmatimonas and an unclassified member of Xanthomonadaceae, were substantially increased by organic-inorganic amendments rather than inorganic amendments only. A co-occurrence based network analysis demonstrated that SOC and TN had strong positive associations with some taxa (Gemmatimonas and the members of Acidobacteria subgroup 6, Myxococcales, Betaproteobacteria and Bacteroidetes), and Gemmatimonas, Flavobacterium and an unclassified member of Verrucomicrobia were identified as the keystone taxa. These specific taxa identified above are implicated in the decomposition of complex organic matters and soil carbon, nitrogen and phosphorus transformations. The present work strengthens our current understanding of the soil microbial community structure and functions under long-term fertilization management and provides certain theoretical support for selection of rational fertilization strategies.
238 citations
Cites background or result from "Short-term effects of organic and i..."
...It was observed even that bacterial growth and community structure were changed in a short time period by a small fraction of organic component in the total amount of fertilizers applied (Lazcano et al., 2013)....
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...Similar results were reported previously, based on the phospholipid fatty acid analysis (Lazcano et al., 2013; Williams et al., 2013)....
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...…plant disease suppression, or disease incidence, etc., Increasing the sustainability of cropping systems involves the reduced inputs of agrochemical fertilizers and combined organic amendments to facilitate biological interactions for the provision of plant nutrients (Lazcano et al., 2013)....
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..., Increasing the sustainability of cropping systems involves the reduced inputs of agrochemical fertilizers and combined organic amendments to facilitate biological interactions for the provision of plant nutrients (Lazcano et al., 2013)....
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TL;DR: It is suggested that the fungal and bacterial communities respond differently to the long-term organic-inorganic fertilization, which may result from different effects of NO3−-N/OM content of soil on the composition of fungaland bacterial communities.
Abstract: The use of organic compost combined with inorganic fertilizer can enable balanced fertilization under intensive farming conditions, but little is known about how these fertilization practices affect the composition of microbial in arable soils. In this study, a field trial of a rice–wheat cropping system was established to examine the effects of 8 years of fertilization with inorganic fertilizers (IFs) and the organic manure–inorganic fertilizers (OMIFs) on composition of microbial communities. The fungal 18S and bacterial 16S rRNA gene fragments were amplified from each soil sample and sequenced. Significantly lower fungal richness and higher bacterial richness were observed for the OMIF treatment compared to the other treatments. No obvious changes in fungal diversity were observed among the treatments, with a decrease bacterial diversity detected in the IF treatment. Variations in relative abundance were observed in the fungal phyla Glomeromycota, Blastocladiomycota, and Schizoplasmodiida and in the bacterial phyla Acidobacteria, Gemmatimonadetes, and Cyanobacteria, most of which were significantly correlated with soil organic matter (OM) and/or nitrate N (NO3
−-N) contents. Additionally, the fungal abundance-based coverage estimator (ACE) showed a significant negative correlation with the soil NO3
−-N/OM content, while the correlation was positive for the bacterial ACE estimate. This study suggests that the fungal and bacterial communities respond differently to the long-term organic-inorganic fertilization, which may result from different effects of NO3
−-N/OM content of soil on the composition of fungal and bacterial communities.
180 citations
Cites background from "Short-term effects of organic and i..."
...Furthermore, bacterial proliferation following the increase of labile organic substrates had antagonistic effects on fungal growth (Lazcano et al. 2013)....
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TL;DR: Overall, inoculations with Trichoderma may be considered as a viable strategy to manage the nutrient content of leafy horticulture crops cultivated in low fertility soils, and assist vegetable growers in reducing the use of synthetic fertilizers, developing sustainable management practices to optimize N use efficiency.
Abstract: Microbial inoculants such as Trichoderma-based products are receiving great interest among researchers and agricultural producers for their potential to improve crop productivity, nutritional quality as well as resistance to plant pathogens/pests and numerous environmental stresses. Two greenhouse experiments were conducted to assess the effects of Trichoderma-based biostimulants under suboptimal, optimal and supraoptimal levels of nitrogen (N) fertilization in two leafy vegetables: Iceberg lettuce (Lactuca sativa L.) and rocket (Eruca sativa Mill.). The yield, nutritional characteristics, N uptake and mineral composition were analyzed for each vegetable crop after inoculation with Trichoderma strains T. virens (GV41) or T. harzianum (T22), and results were compared to non-inoculated plants. In addition, the effect of the Trichoderma-based biostimulants on microbes associated with the rhizosphere in terms of prokaryotic and eurkaryotic composition and concentration using DGGE was also evaluated. Trichoderma-based biostimulants, in particular GV41, positively increased lettuce and rocket yield in the unfertilized plots. The highest marketable lettuce fresh yield was recorded with either of the biostimulant inoculations when plants were supplied with optimal levels of N. The inoculation of rocket with GV41, and to a lesser degree with T22, elicited an increase in total ascorbic acid under both optimal and high N conditions. T. virens GV41 increased N-use efficiency of lettuce, and favoured the uptake of native N present in the soil of both lettuce and rocket. The positive effect of biostimulants on nutrient uptake and crop growth was species-dependent, being more marked with lettuce. The best biostimulation effects from the Trichoderma treatments were observed in both crops when grown under low N availability. The Trichoderma inoculation strongly influenced the composition of eukaryotic populations in the rhizosphere, in particularly exerting different effects with low N levels in comparison to the N fertilized plots. Overall, inoculations with Trichoderma may be considered as a viable strategy to manage the nutrient content of leafy horticulture crops cultivated in low fertility soils, and assist vegetable growers in reducing the use of synthetic fertilizers, developing sustainable management practices to optimize N use efficiency.
175 citations
Cites background from "Short-term effects of organic and i..."
...…in native bacterial and fungal rhizosphere populations could be due to the fact that bacteria are generally more sensitive to any environmental changes since they have a much shorter generation time than fungi, and therefore can respond more quickly to soil amendments (Lazcano et al., 2013)....
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References
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01 Aug 2002
7,234 citations
"Short-term effects of organic and i..." refers background in this paper
...The number of dimensions needed to distinguish among the treatments is identified by the number of significant canonical discriminant functions (McCune and Grace 2002)....
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TL;DR: Results from principal component analysis showed that determining the levels of fatty acids present in both low and high concentrations is essential in order to correctly identify microorganisms and accurately classify them into taxonomically defined groups.
Abstract: This review discusses the analysis of whole-community phospholipid fatty acid (PLFA) profiles and the composition of lipopolysaccharides in order to assess the microbial biomass and the community structure in soils. For the determination of soil microbial biomass a good correlation was obtained between the total amount of PLFAs and the microbial biomass measured with methods commonly used for determinations such as total adenylate content and substrate-induced respiration. Generally, after the application of multivariate statistical analyses, whole-community fatty acid profiles indicate which communities are similar or different. However, in most cases, the organisms accounting for similarity or difference cannot be determined, and therefore artefacts could not be excluded. The fatty acids used to determine the biomass vary from those which determine the community structure. Specific attention has to be paid when choosing extraction methods in order to avoid the liberation of fatty acids from non-living organic material and deposits, and to exclude the non-target selection of lipids from living organisms, as well. By excluding the fatty acids which were presumed to be common and widespread prior to multivariate statistical analysis, estimates were improved considerably. Results from principal component analysis showed that determining the levels of fatty acids present in both low and high concentrations is essential in order to correctly identify microorganisms and accurately classify them into taxonomically defined groups. The PLFA technique has been used to elucidate different strategies employed by microorganisms to adapt to changed environmental conditions under wide ranges of soil types, management practices, climatic origins and different perturbations. It has been proposed that the classification of PLFAs into a number of chemically different subgroups should simplify the evaluating procedure and improve the assessment of soil microbial communities, since then only the subgroups assumed to be involved in key processes would be investigated.
1,895 citations
"Short-term effects of organic and i..." refers methods in this paper
...Certain PLFAs were used as biomarkers to determine the presence and abundance of specific microbial groups (Zelles 1997, 1999)....
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