Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank

Leite, Márcio Fernandes Alves; Pan, Yao; Bloem, J.; Berge, Hein ten; Kuramae, Eiko E.

doi:10.1038/srep42634

Cited by 50 publications

(24 citation statements)

References 62 publications

(79 reference statements)

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“…Short-term organic fertilizers could have significant influences on soil fungal community structures. Clustering and PCoA analysis revealed visible changes in the fungal community compositions due to the different amendments (Figure 3a,b), which is consistent with previous results [21,22]. Ascomycota were significantly higher in term of relative abundance in soil amended with M and MS at both time points (Figure 4; Table S2).…”

Section: Discussionsupporting

confidence: 90%

“…However, most of the researchers have studied the response of fungal communities to organic materials in term of different types in soil ecosystems under long-term experiments [19,20]. Only a few studies were carried out in order to investigate the impacts of organic materials on soil fungal community structure and soil fertility under short-term experiments [21,22], which are supposed to be very different from long-term ones. In our previous study, we explored the impacts of sugarcane straw (S), goat manure (M), and goat manure plus sugarcane straw (MS) on soil fertility, soil enzymes activities, and bacterial composition at two different time points.…”

Section: Introductionmentioning

confidence: 99%

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Short-Term Effects of Different Organic Amendments on Soil Fungal Composition

et al. 2019

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Fungi play an essential role in recovering the quality and fertility of soil. There is a limited understating of the complex response of fungal diversity to different organic materials in clay loam soil. Here, we report the response of soil fungi toward the short-term application of manure (M), sugarcane straw (S), and sugarcane straw plus manure (MS), including no organic material control (CK) at two different time points (50 and 100 days after application). Illumina sequencing was used to examine the fungal communities. Our results reveal a significant shift among the soil fungal community structure associated with each organic material application. After both time points, amendments—especially M and MS—decreased the fungal richness and stimulated the copiotrophic fungal group (Ascomycota) compared to the control soil (CK) and S-amended soil. On the contrary, as compared to the M and MS-amended soils, the CK and S-amended soils at both time points increased the fungal richness and stimulated the oligotrophic fungal groups. Organic material use, especially M and MS, showed variable results regarding pathogenic fungi enhancing the abundance of Lophodermium and Cercophora and decreasing Fusarium. Concerning the abundance of plant-beneficial fungi, Mortierella was reduced, and Podospora was increased by M and MS input. FUNGuild showed that the amendment of organic materials efficiently declined the abundance of endophytes and plant pathogens, but also enhanced the animal pathogens in terms of abundance with respect to CK at two time points. This study could be useful to provide a novel understanding of the management of soil-borne pathogens by organic amendments for the sustainable production of short-term crops.

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Section: Discussionsupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Short-Term Effects of Different Organic Amendments on Soil Fungal Composition

et al. 2019

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“…Members of Nitrospira are mostly uncultured nitrite-oxidizing bacteria ( Palomo et al, 2016 ). In this study, Nitrospira OTUs were more relevant to the CFM than to the CF treatment in the topsoil, probably due to the lower C/N ratio of manure, which mobilizes soil N, increases its mineralization and the availability of mineral nitrogen ( Leite et al, 2017 ).…”

Section: Discussionmentioning

confidence: 71%

Long-term Fertilization Structures Bacterial and Archaeal Communities along Soil Depth Gradient in a Paddy Soil

Wang

Shen

et al. 2017

Front. Microbiol.

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Soil microbes provide important ecosystem services. Though the effects of changes in nutrient availability due to fertilization on the soil microbial communities in the topsoil (tilled layer, 0–20 cm) have been extensively explored, the effects on communities and their associations with soil nutrients in the subsoil (below 20 cm) which is rarely impacted by tillage are still unclear. 16S rRNA gene amplicon sequencing was used to investigate bacterial and archaeal communities in a Pup-Calric-Entisol soil treated for 32 years with chemical fertilizer (CF) and CF combined with farmyard manure (CFM), and to reveal links between soil properties and specific bacterial and archaeal taxa in both the top- and subsoil. The results showed that both CF and CFM treatments increased soil organic carbon (SOC), soil moisture (MO) and total nitrogen (TN) while decreased the nitrate_N content through the profile. Fertilizer applications also increased Olsen phosphorus (OP) content in most soil layers. Microbial communities in the topsoil were significantly different from those in subsoil. Compared to the CF treatment, taxa such as Nitrososphaera, Nitrospira, and several members of Acidobacteria in topsoil and Subdivision 3 genera incertae sedis, Leptolinea, and Bellilinea in subsoil were substantially more abundant in CFM. A co-occurrence based network analysis demonstrated that SOC and OP were the most important soil parameters that positively correlated with specific bacterial and archaeal taxa in topsoil and subsoil, respectively. Hydrogenophaga was identified as the keystone genus in the topsoil, while genera Phenylobacterium and Steroidobacter were identified as the keystone taxa in subsoil. The taxa identified above are involved in the decomposition of complex organic compounds and soil carbon, nitrogen, and phosphorus transformations. This study revealed that the spatial variability of soil properties due to long-term fertilization strongly shapes the bacterial and archaeal community composition and their interactions at both high and low taxonomic levels across the whole soil profile.

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“…Short- and long-term impacts of inorganic fertilization practices on soil microbial community structure have been reported [ 7 – 11 ]. However, few studies have evaluated the impact of organic fertilizer on the resident soil bacterial community, particularly immediately after application and throughout the plant-growing season [ 10 , 12 ]. Organic fertilizers directly or indirectly cause small-scale disturbances of soil habitats due to their water content, chemical and organic components, and introduction of exogenous microbes (depending on the feedstock source) [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

Resilience of the resident soil microbiome to organic and inorganic amendment disturbances and to temporary bacterial invasion

et al. 2018

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BackgroundVinasse, a by-product of sugarcane ethanol production, is recycled by sugarcane plantations as a fertilizer due to its rich nutrient content. However, the impacts of the chemical and microbial composition of vinasse on soil microbiome dynamics are unknown. Here, we evaluate the recovery of the native soil microbiome after multiple disturbances caused by the application of organic vinasse residue, inorganic nitrogen, or a combination of both during the sugarcane crop-growing season (389 days). Additionally, we evaluated the resistance of the resident soil microbial community to the vinasse microbiome.ResultsVinasse applied alone or 30 days prior to N resulted in similar changes in the soil microbial community. Furthermore, the impact of the application of vinasse together with N fertilizer on the soil microbial community differed from that of N fertilizer alone. Organic vinasse is a source of microbes, nutrients, and organic matter, and the combination of these factors drove the changes in the resident soil microbial community. However, these changes were restricted to a short period of time due to the capacity of the soil community to recover. The invasive bacteria present in the vinasse microbiome were unable to survive in the soil conditions and disappeared after 31 days, with the exception of the Acetobacteraceae (native in the soil) and Lactobacillaceae families.ConclusionOur analysis showed that the resident soil microbial community was not resistant to vinasse and inorganic N application but was highly resilient.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0525-1) contains supplementary material, which is available to authorized users.

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Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank

Cited by 50 publications

References 62 publications

Short-Term Effects of Different Organic Amendments on Soil Fungal Composition

Short-Term Effects of Different Organic Amendments on Soil Fungal Composition

Long-term Fertilization Structures Bacterial and Archaeal Communities along Soil Depth Gradient in a Paddy Soil

Resilience of the resident soil microbiome to organic and inorganic amendment disturbances and to temporary bacterial invasion

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