Metaproteome of the microbial community in paddy soil after long-term treatment with mineral and organic fertilizers

2015 ◽  
Vol 61 (3-4) ◽  
pp. 146-156 ◽  
Author(s):  
Yun Wu ◽  
Chuan-Hai Li ◽  
Juan Zhao ◽  
Yong-Liang Xiao ◽  
Hui Cao
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Paddy Soil ◽  
Soil Microbial Communities ◽  
Organic Fertilizers ◽  
Community Research ◽  
Pig Manure ◽  
Soil Microbial ◽  
Long Term Treatment

The soil microbial community research conducted in the field has focused on the genetic diversity of these organisms. In this study, we assessed the proteins expressed in soil microbial communities following the long-term application of mineral fertilizer (NPK) and organic manure (M) to paddy soil, indirect extraction method and separated via two-dimensional (2D) gel electrophoresis and identified using a matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) approach. We found that the number of cells in the primary soil in the M treatment was significantly greater than in the NPK and CK treatments. The numbers of cells extracted were consistent with the total cell numbers and the concentration of extracted proteins (CK < NPK < M). 303 and 306 protein spots being detected in the CK map and NPK map, respectively. Eleven spots of interest were identified in the 2D gels, including 8 different protein spots and 3 unique protein spots. Three common proteins involved in protein hydrolysis and glutamate synthesis and metabolism. Eight differentially expressed proteins involved in DNA replication, transcription, protein folding and energy metabolism, the processes of cofactor and vitamin metabolism, transcriptional regulation, recombination and xenobiotic compound biodegradation and metabolism. The long-term application of fertilization resulted in significant changes in the microbial community structure and function, and the long-term application of pig manure significantly increased the microbial biomass and the functional and structural diversity in the soil. It is very interesting to address the MS identification of intracellular proteins from microbial communities under different fertilizer treatments in a paddy soil.

Impacts of long-term fertilization on the soil microbial communities in double-cropped paddy fields

2018 ◽  
Vol 156 (7) ◽  
pp. 857-864 ◽  
Author(s):  
H. M. Tang ◽  
Y. L. Xu ◽  
X. P. Xiao ◽  
C. Li ◽  
W. Y. Li ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Soil Microbial Communities ◽  
Chemical Fertilizer ◽  
Soil Microbial Community Structure ◽  
Soil Microbial

AbstractThe response of soil microbial communities to soil quality changes is a sensitive indicator of soil ecosystem health. The current work investigated soil microbial communities under different fertilization treatments in a 31-year experiment using the phospholipid fatty acid (PLFA) profile method. The experiment consisted of five fertilization treatments: without fertilizer input (CK), chemical fertilizer alone (MF), rice (Oryza sativaL.) straw residue and chemical fertilizer (RF), low manure rate and chemical fertilizer (LOM), and high manure rate and chemical fertilizer (HOM). Soil samples were collected from the plough layer and results indicated that the content of PLFAs were increased in all fertilization treatments compared with the control. The iC15:0 fatty acids increased significantly in MF treatment but decreased in RF, LOM and HOM, while aC15:0 fatty acids increased in these three treatments. Principal component (PC) analysis was conducted to determine factors defining soil microbial community structure using the 21 PLFAs detected in all treatments: the first and second PCs explained 89.8% of the total variance. All unsaturated and cyclopropyl PLFAs except C12:0 and C15:0 were highly weighted on the first PC. The first and second PC also explained 87.1% of the total variance among all fertilization treatments. There was no difference in the first and second PC between RF and HOM treatments. The results indicated that long-term combined application of straw residue or organic manure with chemical fertilizer practices improved soil microbial community structure more than the mineral fertilizer treatment in double-cropped paddy fields in Southern China.

scholarly journals The Effects of Soil Depth on the Structure of Microbial Communities in Agricultural Soils in Iowa, USA

2020 ◽  
Author(s):  
Jingjie Hao ◽  
Yen Ning Chai ◽  
Lucas Dantas Lopes ◽  
Raziel A. Ordóñez ◽  
Emily E. Wright ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Agricultural Soils ◽  
Soil Depth ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Deep Soil ◽  
Soil Microbial ◽  
Deep Soils

This study investigated the differences in microbial community abundance, composition and diversity throughout the depth profiles in soils collected from corn and soybean fields in lowa, USA using 16S rRNA amplicon sequencing. The results revealed decreased richness and diversity in microbial communities at increasing soil depth. Soil microbial community composition differed due to crop type only in the top 60 cm and due to location only in the top 90 cm. While the relative abundance of most phyla decreased in deep soils, the relative abundance of the phylum Proteobacteria increased and dominated agricultural soils below the depth of 90 cm. Although soil depth was the most important factor shaping microbial communities, edaphic factors including soil organic matter, soil bulk density and the length of time that deep soils were saturated with water were all significant factors explaining the variation in soil microbial community composition. Soil organic matter showed the highest correlation with the exponential decrease in bacterial abundance with depth. A greater understanding of how soil depth influences the diversity and composition of soil microbial communities is vital for guiding sampling approaches in agricultural soils where plant roots extend beyond the upper soil profile. In the long term a greater knowledge of the influence of depth on microbial communities should contribute to new strategies that enhance the sustainability of soil which is a precious resource for food security. IMPORTANCE Determining how microbial properties change across different soils and within the soil depth profile, will be potentially beneficial to understanding the long-term processes that are involved in the health of agricultural ecosystems. Most literature on soil microbes has been restricted to the easily accessible surface soils. However, deep soils are important in soil formation, carbon sequestration, and in providing nutrients and water for plants. In the most productive agricultural systems in the USA where soybean and corn are grown, crop plant roots extend into the deeper regions of soils (> 100 cm), but little is known about the taxonomic diversity or the factors that shape deep soil microbial communities. The findings reported here highlight the importance of soil depth in shaping microbial communities, provide new information about edaphic factors that influence the deep soil communities and reveal more detailed information on taxa that exist in deep agricultural soils.

scholarly journals Long-Term Effects of Perfluorooctanoic Acid (PFOA) and Perfluorooctane Sulfonic Acid (PFOS) on Soil Microbial Community

2021 ◽  
Author(s):  
Wan Tao ◽  
Rui Xu ◽  
Hanzhi Lin ◽  
Duanyi Huang ◽  
Pingzhou Su ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Gene Prediction ◽  
Soil Microbial Communities ◽  
Alpha Diversity ◽  
Perfluorooctanoic Acid ◽  
Long Term Effects ◽  
Soil Microbial

Abstract The extensive application of perfluoroalkyl and polyfluoroalkyl substances (PFASs) causes their frequent detection in various environments. Nevertheless, the effects of PFASs exposure on environmental microorganisms still remain unknown. In current work, two typical PFASs, perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), are selected to investigate their long-term effects on soil microbes. Microbial community structure and diversity were investigated by high-throughput sequencing and multiple statistical methods. Under 90-days of exposure, PFAS treatments increased the alpha-diversity of soil microbial communities with PFOS treatment, followed by PFOA treatment. The long-term exposure of PFASs substantially changed the compositions of soil microbial communities. The most abundant phylum Proteobacteria decreased from 82.9% (without amended PFASs) to 62.1% (with PFOA treatment) and 77.8% (with PFOS treatment). As a comparison, the relative abundance of Bacteroidetes, Chloroflexi, Acidobacteria, and Ignavibacteriae increased in the PFOA or PFOS groups. Comparative co-occurrence networks were constructed to investigate the biotic interactions in the two treatments. It was found that most taxonomy nodes in the PFOA and PFOS networks were associated with the genus Hydrogenophaga and Pseudoxanthomonas, respectively. The LEfSe analysis identified a set of core taxonomies (e.g., Azospirillum, Methyloversatilis, Ancylobacter, Hydrogenophaga, and Methylomonas) in the soil microbial communities and suggested their different preferences to PFAS exposures. Functional gene prediction suggested that the microbial metabolism processes, such as nucleotide transport and metabolism, cell motility, carbohydrate transport and metabolism, energy production and conversion, and secondary metabolites biosynthesis transport and catabolism, might be significantly inhibited under PFAS exposure, which may further affect soil ecological services.

scholarly journals Adaptation to chronic drought modifies soil microbial community responses to phytohormones

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Emma J. Sayer ◽  
John A. Crawford ◽  
James Edgerley ◽  
Andrew P. Askew ◽  
Christoph Z. Hahn ◽  
...  
Keyword(s):  
Microbial Community ◽  
Soil Respiration ◽  
Microbial Communities ◽  
Soil Microbial Community ◽  
Plant Stress ◽  
Soil Microbial Communities ◽  
Community Responses ◽  
Soil Microbial ◽  
Plant Soil

AbstractDrought imposes stress on plants and associated soil microbes, inducing coordinated adaptive responses, which can involve plant–soil signalling via phytohormones. However, we know little about how microbial communities respond to phytohormones, or how these responses are shaped by chronic (long-term) drought. Here, we added three phytohormones (abscisic acid, 1-aminocyclopropane-1-carboxylic acid, and jasmonic acid) to soils from long-term (25-year), field-based climate treatments to test the hypothesis that chronic drought alters soil microbial community responses to plant stress signalling. Phytohormone addition increased soil respiration, but this effect was stronger in irrigated than in droughted soils and increased soil respiration at low phytohormone concentrations could not be explained by their use as substrate. Thus, we show that drought adaptation within soil microbial communities modifies their responses to phytohormone inputs. Furthermore, distinct phytohormone-induced shifts in microbial functional groups in droughted vs. irrigated soils might suggest that drought-adapted soil microorganisms perceive phytohormones as stress-signals, allowing them to anticipate impending drought.

scholarly journals Comparison of Drivers of Soil Microbial Communities Developed in Karst Ecosystems with Shallow and Deep Soil Depths

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 173
Author(s):  
Huiling Guan ◽  
Jiangwen Fan ◽  
Haiyan Zhang ◽  
Warwick Harris
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Soil Depth ◽  
Phospholipid Fatty Acid ◽  
Soil Microbial Communities ◽  
Deep Soil ◽  
Soil System ◽  
Soil Microbial ◽  
Total Soil ◽  
Karst Ecosystems

Soil erosion is prevalent in karst areas, but few studies have compared the differences in the drivers for soil microbial communities among karst ecosystems with different soil depths, and most studies have focused on the local scale. To fill this research gap, we investigated the upper 20 cm soil layers of 10 shallow–soil depth (shallow–SDC, total soil depth less than 100 cm) and 11 deep–soil depth communities (deep–SDC, total soil depth more than 100 cm), covering a broad range of vegetation types, soils, and climates. The microbial community characteristics of both the shallow–SDC and deep–SDC soils were tested by phospholipid fatty acid (PLFAs) analysis, and the key drivers of the microbial communities were illustrated by forward selection and variance partitioning analysis. Our findings demonstrated that more abundant soil nutrients supported higher fungal PLFA in shallow–SDC than in deep–SDC (p < 0.05). Furthermore, stronger correlation between the microbial community and the plant–soil system was found in shallow–SDC: the pure plant effect explained the 43.2% of variance in microbial biomass and 57.8% of the variance in the ratio of Gram–positive bacteria to Gram–negative bacteria (G+/G−), and the ratio of fungi to total bacteria (F/B); the pure soil effect accounted for 68.6% variance in the microbial diversity. The ratio of microbial PLFA cyclopropyl to precursors (Cy/Pr) and the ratio of saturated PLFA to monounsaturated PLFA (S/M) as indicators of microbial stress were controlled by pH, but high pH was not conducive to microorganisms in this area. Meanwhile, Cy/Pr in all communities was >0.1, indicating that microorganisms were under environmental stress. Therefore, the further ecological restoration of degraded karst communities is needed to improve their microbial communities.

scholarly journals Responses of soil microbial communities and enzyme activities to nitrogen and phosphorus additions in Chinese fir plantations of subtropical China

2015 ◽  
Vol 12 (13) ◽  
pp. 10359-10387 ◽  
Author(s):  
W. Y. Dong ◽  
X. Y. Zhang ◽  
X. Y. Liu ◽  
X. L. Fu ◽  
F. S. Chen ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Enzyme Activities ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Chinese Fir ◽  
Subtropical China ◽  
Nitrogen And Phosphorus ◽  
Soil Microbial ◽  
Nutrient Additions

Abstract. Nitrogen (N) and phosphorus (P) additions to forest ecosystems are known to influence various above-ground properties, such as plant productivity and composition, and below-ground properties, such as soil nutrient cycling. However, our understanding of how soil microbial communities and their functions respond to nutrient additions in subtropical plantations is still not complete. In this study, we added N and P to Chinese fir plantations in subtropical China to examine how nutrient additions influenced soil microbial community composition and enzyme activities. The results showed that most soil microbial properties were responsive to N and/or P additions, but responses often varied depending on the nutrient added and the quantity added. For instance, there were more than 30 % greater increases in the activities of β-Glucosidase (βG) and N-acetyl-β-D-glucosaminidase (NAG) in the treatments that received nutrient additions compared to the control plot, whereas acid phosphatase (aP) activity was always higher (57 and 71 %, respectively) in the P treatment. N and P additions greatly enhanced the PLFA abundanceespecially in the N2P treatment, the bacterial PLFAs (bacPLFAs), fungal PLFAs (funPLFAs) and actinomycic PLFAs (actPLFAs) were about 2.5, 3 and 4 times higher, respectively, than in the CK. Soil enzyme activities were noticeably higher in November than in July, mainly due to seasonal differences in soil moisture content (SMC). βG or NAG activities were significantly and positively correlated with microbial PLFAs. There were also significant relationships between gram-positive (G+) bacteria and all three soil enzymes. These findings indicate that G+ bacteria is the most important microbial community in C, N, and P transformations in Chinese fir plantations, and that βG and NAG would be useful tools for assessing the biogeochemical transformation and metabolic activity of soil microbes. We recommend combined additions of N and P fertilizer to promote soil fertility and microbial activity in this kind of plantation.

scholarly journals STRUKTUR KOMUNITAS MIKROBA TANAH DAN IMPLIKASINYA DALAM MEWUJUDKAN SISTEM PERTANIAN BERKELANJUTAN

el–Hayah ◽  
2012 ◽  
Vol 1 (4) ◽  
Author(s):  
Prihastuti Prihastuti
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Soil Microbial Community ◽  
Soil Microbial Communities ◽  
Organic Soil ◽  
Plant Type ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Wide Range

<p>Soils are made up of organic and an organic material. The organic soil component contains all the living creatures in the soil and the dead ones in various stages of decomposition.  Biological activity in soil helps to recycle nutrients, decompose organic matter making nutrient available for plant uptake, stabilize humus, and form soil particles.<br />The extent of the diversity of microbial in soil is seen to be critical to the maintenance of soil health and quality, as a wide range of microbial is involved in important soil functions.  That ecologically managed soils have a greater quantity and diversity of soil microbial. The two main drivers of soil microbial community structure, i.e., plant type and soil type, are thought to exert their function in a complex manner. The fact that in some situations the soil and in others the plant type is the key factor determining soil microbial diversity is related to their complexity of the microbial interactions in soil, including interactions between microbial and soil and microbial and plants. <br />The basic premise of organic soil stewardship is that all plant nutrients are present in the soil by maintaining a biologically active soil environment. The diversity of microbial communities has on ecological function and resilience to disturbances in soil ecosystems. Relationships are often observed between the extent of microbial diversity in soil, soil and plant quality and ecosystem sustainability. Agricultural management can be directed toward maximizing the quality of the soil microbial community in terms of disease suppression, if it is possible to shift soil microbial communities.</p><p>Keywords: structure, microbial, implication, sustainable agriculture<br /><br /></p>

Soil bacterial communities interact with silicon fraction transformation and promote rice yield after long-term straw return

2021 ◽  
Author(s):  
Alin Song ◽  
Zimin Li ◽  
Fenliang Fan
Keyword(s):  
Microbial Community ◽  
Rice Yield ◽  
Soil Microbial Communities ◽  
Nutrient Sources ◽  
Soil Microbial ◽  
Mn Oxide ◽  
Straw Return ◽  
Soil Bacterial ◽  
Healthy Growth

&lt;p&gt;Returning crop straw into soil is an important practice to balance biogenic and bioavailable silicon (Si) pool in paddy, which is crucial for rice healthy growth. However, it remains elusive how straw return affects Si bioavailability, its uptake, and rice yield, owing to little knowledge about soil microbial communities responsible for straw degradation. Here, we investigated the change of soil Si fractions and microbial community in a 39-year-old paddy field amended by a long-term straw return. Results showed that rice straw-return significantly increased soil bioavailable Si and rice yield to from 29.9% to 61.6% and from 14.5% to 23.6%, respectively, compared to NPK fertilization alone. Straw return significantly altered soil microbial community abundance. Acidobacteria was positively and significantly related to amorphous Si, while Rokubacteria at the phylum level, Deltaproteobacteria and Holophagae at the class level were negatively and significantly related to organic matter adsorbed and Fe/Mn-oxide combined Si in soils. Redundancy analysis of their correlations further demonstrated that Si status significantly explained 12% of soil bacterial community variation. These findings suggest that soil bacteria community and diversity interact with Si mobility via altering its transformation, resulting in the balance of various nutrient sources to drive biological silicon cycle in agroecosystem.&lt;/p&gt;

Distinct assembly processes and determinants of soil microbial communities between farmland and grassland in arid and semiarid areas

2021 ◽  
Author(s):  
Aiai Xu ◽  
Jie Liu ◽  
Zhiying Guo ◽  
Changkun Wang ◽  
Kai Pan ◽  
...  
Keyword(s):  
Microbial Community ◽  
Variable Selection ◽  
Microbial Communities ◽  
Soil Microbial Community ◽  
Environmental Gradient ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
Semiarid Areas ◽  
Arid And Semiarid Areas ◽  
Arid And Semiarid

It is critical to identify the assembly processes and determinants of soil microbial communities to better predict soil microbial responses to environmental change in arid and semiarid areas. Here, soils from 16 grassland-only, 9 paired grassland and farmland, and 16 farmland-only sites were collected across the central Inner Mongolia Plateau covering a steep environmental gradient. Through analyzing the paired samples, we discovered that land uses had strong effects on soil microbial communities, but weak effects on their assembly processes. For all samples, although no environmental variables were significantly correlated with the net relatedness index (NRI), both the nearest taxon index (NTI) and the β-nearest taxon index (βNTI) were most related to mean annual precipitation (MAP). With the increase of MAP, soil microbial taxa at the tips of the phylogenetic tree were more clustered, and the contribution of determinism increased. Determinism (48.6%), especially variable selection (46.3%), and stochasticity (51.4%) were almost equal in farmland, while stochasticity (75.0%) was dominant in grassland. Additionally, Mantel tests and redundancy analyses (RDA) revealed that the main determinants of soil microbial community structure were MAP in grassland, but mean annual temperature (MAT) in farmland. MAP and MAT were also good predictors of the community composition (the top 200 dominant OTUs) in grassland and farmland, respectively. Collectively, in arid and semiarid areas, soil microbial communities were more sensitive to environmental change in farmland than in grassland, and unlike the major impact of MAP on grassland microbial communities, MAT was the primary driver of farmland microbial communities. Importance As one of the most diverse organisms, soil microbes play indispensable roles in many ecological processes in arid and semiarid areas with limited macrofaunal and plant diversity, yet the mechanisms underpinning soil microbial community are not fully understood. In this study, soil microbial communities were investigated along a 500 km transect covering a steep environmental gradient across farmland and grassland in the areas. The results showed that precipitation was the main factor mediating the assembly processes. Determinism was more influential in farmland, and variable selection of farmland was twice that of grassland. Temperature mainly drove farmland microbial communities, while precipitation mainly affected grassland microbial communities. These findings provide new information about the assembly processes and determinants of soil microbial communities in arid and semiarid areas, consequently improving the predictability of the community dynamics, which have implications for sustaining soil microbial diversity and ecosystem functioning, particularly under global climate change conditions.

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