Shifts in Nitrobacter- and Nitrospira-like nitrite-oxidizing bacterial communities under long-term fertilization practices

Han, Shun; Zeng, Luyang; Luo, Xuesong; Xiong, Xiang; Wen, Shilin; Wang, Boren; Chen, Wenli; Huang, Qiaoyun

doi:10.1016/j.soilbio.2018.05.033

Cited by 74 publications

(39 citation statements)

References 45 publications

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“…Nitrospira is the most widespread and well-known nitrite-oxidizing bacteria (NOB) [31], which plays an important role in the soil nitrogen (N) cycle [32]. In this test, Nitrospira accounted for the highest proportion in each sample, this indicates that Nitrospira was the dominant genus of bacteria in the samples, which is consistent with the research conclusions done by Tobin et al [33].…”

Section: Discussionsupporting

confidence: 88%

Response of Soil Microbes to Vegetation Restoration in Coal Mining Subsidence Areas at Huaibei Coal Mine, China

Sun

Deshun

et al. 2019

IJERPH

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Vegetation restoration is an available way to ameliorate degraded lands. In order to study the response of soil microbes to vegetation restoration in coal mining subsidence areas, the composition and distribution of soil microbes were discussed through three plots: unsubsided area (CA), new subsided area (NSA), and old subsided area (OSA) with different vegetation restoration time in Huabei coal mine. Meanwhile, changes in soil catalase and urease activity were explored and the correlation between soil bacteria, fungi, and environmental factors was analysed. The results demonstrated that Nitrospira was the dominant bacteria in all areas sampled. Microorganisms in the 0–20 cm and 40–60 cm soil layers of OSA had the highest Simpson index, whereas the index in NSA was lowest (at all soil depths). The catalase activity in NSA was significantly higher than that in CA, and there was no significant difference in catalase activity with soil depth, while the urease activity declined gradually with increasing soil depth. The urease activity in the 20–60 cm soil layer of NSA and OSA was significantly higher than that of CA. Furthermore, the distribution of bacteria was mainly affected by soil organic matter, available potassium, available phosphorus, and alkali-hydrolyzable nitrogen, whereas pH and catalase activity mainly affected fungal distribution. These results implied that soil catalase activity in NSA and urease activity in the 20–40 cm soil layer of NSA and OSA were significantly enhanced after vegetation restoration, and that long-term plant restoration could improve soil fertility and soil microbial community diversity in coal mining areas.

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Section: Discussionsupporting

confidence: 88%

Response of Soil Microbes to Vegetation Restoration in Coal Mining Subsidence Areas at Huaibei Coal Mine, China

Sun

Deshun

et al. 2019

IJERPH

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“…In our study, PNO was not correlated with nxrB gene copy numbers. Several previous studies reported that PNO was strongly and significantly correlated with the abundance of Nitrobacter-like NOB but weakly correlated with the abundance of Nitrospira-like NOB (Attard et al, 2010;Han et al, 2018). Although Nitrobacter were recovered in 16S and metagenomic analysis in our study, their relative abundance was extremely low compared to that of Nitrospira.…”

Section: Discussioncontrasting

confidence: 66%

“…Based on the high-throughput sequencing analysis of Nitrospira nxrB, Nitrospira community composition was significantly changed by ammonium-based fertilizers but not organic fertilizers. However, Han et al (2018) showed that both inorganic and organic fertilization significantly influenced the Nitrospira community composition. Manure, with relatively higher N availability than the compost used in our case, was continuously applied for 26 years in their study.…”

Section: Discussionmentioning

confidence: 96%

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Nitrite Oxidizer Activity and Community Are More Responsive Than Their Abundance to Ammonium-Based Fertilizer in an Agricultural Soil

Ouyang

Norton

2020

Front. Microbiol.

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Autotrophic nitrification is mediated by ammonia oxidizing bacteria (AOB) or ammonia oxidizing archaea (AOA) and nitrite oxidizing bacteria (NOB). Mounting studies have examined the impact of nitrogen (N) fertilization on the dynamic and diversity of AOA and AOB, while we have limited information on the response of the activity, abundance, and diversity of NOB to N fertilization. We investigated the influence of organic and inorganic N fertilizers on soil NOB in silage corn field plots that received contrasting nitrogen (N) treatments: control (no additional N), ammonium sulfate (AS 100 and 200 kg N ha −1), and compost (200 kg N ha −1). Nitrifying community was examined using a universal marker (16S rRNA gene), functional gene markers (AOB amoA and Nitrospira nxrB), and metagenomics. The overall nitrifying community was not altered after the first fertilization but was significantly shifted by 4-year repeated application of ammonium fertilizers. Nitrospira were the dominant NOB (>99.7%) in our agricultural soil. Both community compositions of AOB and Nitrospira were significantly changed by ammonium fertilizers but not by compost after 4 years of repeated applications. All nitrifiers, including comammox, were recovered in soil metagenomes based on a gene-targeted assembly, but their sequence counts were very low. Although N treatment did not affect the abundance of Nitrospira nxrB determined by real-time quantitative PCR, ammonium fertilizers significantly promoted rates of potential nitrite oxidation determined at 0.15 mM nitrite in soil slurries. Understanding the response of both ammonia oxidizers and nitrite oxidizers to N fertilization may initiate or improve strategies for mitigating potential environmental impacts of nitrate production in agricultural ecosystems.

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“…Summary of studies included in the meta-analysis (alphabetical order). Measure Methodology (Balachandar et al, 2014) Tamil Nadu, India Taxonomic 16S seq (Chaudhry et al, 2012 Maharashtra, India Functional Biolog Ecoplate (Chen et al, 2015) Jiangxi, China Functional Biolog Ecoplate (Chen et al, 2016) Jiangsu, China Taxonomic 18S seq (Cui et al, 2018) Hunan, China Taxonomic 16S seq (Ding et al, 2016) Heilongjiang, China Taxonomic 16S seq (Ding et al, 2017) Heilongjiang, China Taxonomic ITS seq (Ge et al, 2008) Fengqiu, China Taxonomic 16S seq (Gu et al, 2009) Sichuan, China Taxonomic 16S DGGE (Guanghua et al, 2008) Jilin, China Taxonomic Functional 16S DGGE Biolog Ecoplate (Hamm et al, 2016) Manitoba, Canada Taxonomic 16S seq (Han et al, 2018) Hunan, China Taxonomic nxr seq (Hu et al, 2018b) Northeast China Taxonomic 16S seq (Ji et al, 2018) Fujian, China Taxonomic 16S seq (Kamaa et al, 2011) Kabete, Kenya Taxonomic 16S and 28S DGGE (Kumar et al, 2017) Odisha, India Functional Biolog Ecoplate (Kumar et al, 2018) Odisha, India Taxonomic 16S seq Shandong, China Taxonomic 16S DGGE (Liu et al, 2015) Jiangxi, China Taxonomic 16S seq (Liu et al, 2019) Hebei, China Taxonomic TRFLP (Mahanta et al, 2017) Uttarakhand, India Taxonomic Soil dilution plate (Nautiyal et al, 2010) Maharashtra, India Functional Biolog Ecoplate (Qiu et al, 2014) Fujian, China Taxonomic 16S and 18S TGGE (Ros et al, 2006) Linz, Austria Taxonomic Functional 16S PGGE Biolog Ecoplate (Sun et al, 2004) Oklahoma, USA Taxonomic 16S DGGE (van Bruggen et al, 2015) Netherlands Taxonomic 16S DGGE (van der Bom et al, 2018) Denmark Taxonomic 16S seq (Wang et al, 2018) Heilongjiang, China Taxonomic 16S seq (Wei et al, 2008) Heilongjiang, China Taxonomic Functional 16S DGGE Biolog Ec...…”

Section: Discussionmentioning

confidence: 99%

A meta-analysis of the effect of organic and mineral fertilizers on soil microbial diversity

Bebber

Richards

2020

Preprint

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The Green Revolution of agriculture was in part driven by application of synthetic mineral fertilizers, largely supplanting organic manure as a source of the major nutrients nitrogen, phosphorous and potassium (NPK). Though enhancing crop production and global food security, fertilizers have contributed to soil acidification, eutrophication of water bodies, and greenhouse gas emissions. Organic agriculture, employing manures or composts, has been proposed as a way of mitigating these undesirable effects. Of particular interest is the effect of fertilizer regime on soil microbes, which are key to nutrient cycling, plant health and soil structure. Meta-analyses of experimental studies indicate that mineral fertilizer increases soil microbial biomass over unfertilized controls, and that organic fertilizers increase microbial biomass and activity over mineral fertilizers. However, the effect of fertilizers on soil microbial diversity remains poorly understood. Since biological diversity is an important determinant of ecosystem function and a fundamental metric in community ecology, the effects of fertilizer regimes on soil microbial diversity are of theoretical and applied interest. Here, we conduct a meta-analysis of 31 studies reporting microbial diversity metrics in mineral fertilized (NPK), organically fertilized (ORG) and unfertilized control (CON) soils. Of these studies, 26 reported taxonomic diversity derived from sequencing, gradient gel electrophoresis, RFLP, or dilution plate assay. Functional diversity, derived from Biolog Ecoplate™ measures of carbon substrate metabolism, was reported in 8 studies, with 3 studies reporting both diversity metrics. We found that functional diversity was on average 2.6 % greater in NPK compared with CON, 6.8 % greater in ORG vs CON and 3.6 % greater in ORG vs NPK. Prokaryote taxonomic diversity was not significantly different between NPK and CON, 4.2 % greater in ORG vs CON and 4.6 % greater in ORG vs. NPK. Fungal taxonomic diversity was not significantly different between NPK or ORG vs CON, but 5.4 % lower between ORG and NPK. There was very high residual heterogeneity in all meta-analyses of soil diversity, suggesting that a large amount of further research with detailed analysis of soil properties is required to fully understand the influence of fertilizer regimes on microbial diversity and ecosystem function.

show abstract

Shifts in Nitrobacter- and Nitrospira-like nitrite-oxidizing bacterial communities under long-term fertilization practices

Cited by 74 publications

References 45 publications

Response of Soil Microbes to Vegetation Restoration in Coal Mining Subsidence Areas at Huaibei Coal Mine, China

Response of Soil Microbes to Vegetation Restoration in Coal Mining Subsidence Areas at Huaibei Coal Mine, China

Nitrite Oxidizer Activity and Community Are More Responsive Than Their Abundance to Ammonium-Based Fertilizer in an Agricultural Soil

A meta-analysis of the effect of organic and mineral fertilizers on soil microbial diversity

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