Spatial Variation in Microbial Community in Response to As and Pb Contamination in Paddy Soils Near a Pb-Zn Mining Site

Mining activity is a growing environmental concern as it contributes to heavy metals (HMs) pollution in agricultural soils. Microbial communities play an important role in the biogeochemical cycling of HMs and have the potential to be used as bioindicators. Arsenic (As) and lead (Pb) are the most hazardous HMs and are mainly originated from mining activities. However, spatial variation in microbial community in response to As and Pb contamination in paddy soils remains overlooked. In this study, the biological and chemical properties of sixteen soil samples from four sites (N01, N02, N03, and N04) near a Pb-Zn mining site at different As and Pb levels were examined. The results showed that soil pH, total As and Pb, bioavailable As and Pb, nitrate-nitrogen (NO3−-N) and ammonia-nitrogen (NH4+-N) were the most important factors in shaping the bacterial community structure. In addition, significant correlations between various bacterial genera and As and Pb concentrations were observed, indicating their potential roles in As and Pb biogeochemical cycling. These findings provide insights into the variation of paddy soil bacterial community in soils co-contaminated with different levels of As and Pb.

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Metagenome analyses reveal the role of Clostridium perfringens in alfalfa silage anaerobic deterioration

FEMS Microbiology Letters ◽

10.1093/femsle/fnaa052 ◽

2020 ◽

Vol 367 (8) ◽

Author(s):

Mingli Zheng ◽

Dongze Niu ◽

Di Jiang ◽

Rongrong Li ◽

Lin Meng ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Clostridium Perfringens ◽

Relative Abundance ◽

Dominant Role ◽

Ammonia Nitrogen ◽

Fermentation Products ◽

Microbial Community Analyses ◽

Alfalfa Silage

ABSTRACT The clostridial fermentation caused by the outgrowth of Clostridia was mainly responsible for the silage anaerobic deterioration. Our previous results showed that Clostridium perfringens dominated the clostridial community in poor-fermented alfalfa silage. This study was conducted to further examine the role of C. perfringens in silage anaerobic deterioration through fermentation products and the microbial community analyses. Direct-cut alfalfa was ensiled with C. perfringens contamination (CKC) or with the addition of Lactobacillus plantarum, sucrose and C. perfringens (LSC). Contamination with C. perfringens enhanced the clostridial fermentation in CKC silage, as indicated by high contents of butyric acid, ammonia nitrogen and Clostridia, while LSC silage was well preserved. The genera Bifidobacterium, Garciella and Clostridium dominated the bacterial community in CKC silage, while predominate genus was replaced by Lactobacillus in LSC silage. The clostridial community in CKC silage was dominated by Garciella sp. (26.9 to 58.1%) and C. tyrobutyricum (24.4 to 48.6%), while the relative abundance of C. perfringens was below 5.0%. Therefore, the effect of Clostridia contamination on ensiling fermentation was dependent on the ensilability of the silage material. Garciella sp. and C. tyrobutyricum, rather than C. perfringens, played dominant role in the clostridial fermentation in CKC silage.

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Differential microbial communities in paddy soils between Guiyang plateaus and Chengdu basins drive the incidence of rice bacterial diseases

Plant Disease ◽

10.1094/pdis-09-21-1974-re ◽

2022 ◽

Author(s):

Yajiao Wang ◽

Shuping Tian ◽

Nan Wu ◽

Wenwen Liu ◽

Li Li ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Microbial Community Composition ◽

Chemical Properties ◽

Ecological Factors ◽

Severity Index ◽

Paddy Soils ◽

Bacterial Diseases ◽

Soil Microbial

Southwest China has the most complex rice-growing regions in China. With great differences in topography, mainly consisting of basins and plateaus, ecological factors in above region differ greatly. In this study, bulk paddy soils collected from a long-term rice field in Chengdu (basins) and in Guiyang (plateaus) were used to study the correlation between microbial diversity and the incidence of rice bacterial diseases. Results showed that the microbial community composition in paddy soils and the microbial functional categories differed significantly between basins and plateaus. They shared more than 70% of the dominant genera (abundance > 1%), but the abundance of the dominant genera differed significantly. Functional analysis found that bulk paddy soils from Chengdu were significantly enriched in virulence factor-related genes; soils from Guiyang were enriched in biosynthesis of secondary metabolites especially antibiotics. Correspondingly, Chengdu was significantly enriched in leaf bacterial pathogens Acidovorax, Xanthomonas, and Pseudomonas. Greenhouse experiments and correlation analysis showed that soil chemical properties had a greater effect on microbial community composition and positively related with the higher incidence of rice bacterial foot rot in Guiyang, while temperature had a greater effect on soil microbial functions and positively related with the higher severity index of leaf bacterial diseases in Chengdu. Our results provide a new perspective on how differences in microbial communities in paddy soils can influence the incidence of rice bacterial diseases in areas with different topographies.

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Effect of Metal-Rich Sludge Amendments on the Soil Microbial Community

Applied and Environmental Microbiology ◽

10.1128/aem.64.1.238-245.1998 ◽

1998 ◽

Vol 64 (1) ◽

pp. 238-245 ◽

Cited By ~ 242

Author(s):

Erland Bååth ◽

Montserrat Díaz-Raviña ◽

Åsa Frostegård ◽

Colin D. Campbell

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Soil Microbial Community ◽

Agricultural Soils ◽

Phospholipid Fatty Acid ◽

Community Based ◽

Soil Microbial ◽

Biolog System ◽

Community Tolerance ◽

Dose Response Effect

ABSTRACT The effects of heavy-metal-containing sewage sludge on the soil microbial community were studied in two agricultural soils of different textures, which had been contaminated separately with three predominantly single metals (Cu, Zn, and Ni) at two different levels more than 20 years ago. We compared three community-based microbiological measurements, namely, phospholipid fatty acid (PLFA) analysis to reveal changes in species composition, the Biolog system to indicate metabolic fingerprints of microbial communities, and the thymidine incorporation technique to measure bacterial community tolerance. In the Luddington soil, bacterial community tolerance increased in all metal treatments compared to an unpolluted-sludge-treated control soil. Community tolerance to specific metals increased the most when the same metal was added to the soil; for example, tolerance to Cu increased most in Cu-polluted treatments. A dose-response effect was also evident. There were also indications of cotolerance to metals whose concentration had not been elevated by the sludge treatment. The PLFA pattern changed in all metal treatments, but the interpretation was complicated by the soil moisture content, which also affected the results. The Biolog measurements indicated similar effects of metals and moisture to the PLFA measurements, but due to high variation between replicates, no significant differences compared to the uncontaminated control were found. In the Lee Valley soil, significant increases in community tolerance were found for the high levels of Cu and Zn, while the PLFA pattern was significantly altered for the soils with high levels of Cu, Ni, and Zn. No effects on the Biolog measurements were found in this soil.

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Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils

10.7287/peerj.preprints.3288v1 ◽

2017 ◽

Author(s):

Craig Anderson ◽

Mike Beare ◽

Hannah L Buckley ◽

Gavin Lear

Keyword(s):

Microbial Community ◽

Agricultural Soils ◽

Microbial Community Composition ◽

Chemical Properties ◽

Community Response ◽

Fungal Communities ◽

Physicochemical Changes ◽

Tillage Depth ◽

Tillage Treatment

In arable cropping systems, reduced or conservation tillage practices are linked with improved soil quality, C retention and higher microbial biomass, but most long-term studies rarely focus on depths greater than 15 cm nor allow comparison of microbial community responses to agricultural practices. We investigated microbial community structure in a long-term field trial (12-years, Lincoln, New Zealand) established in a silt-loam soil over four depth ranges down to 30 cm. Our objectives were to investigate the degree of homogenisation of soil biological and chemical properties with depth, and to determine the main drivers of microbial community response to tillage. We hypothesised that soil microbiological responses would depend on tillage depth, observed by a homogenisation of microbial community composition within the tilled zone. Tillage treatments were mouldboard plough and disc harrow, impacting soil to ~20 and ~10 cm depth, respectively. These treatments were compared to a no-tillage treatment and two control treatments, both permanent pasture and permanent fallow. Bacterial and fungal communities collected from the site were not impacted by the spatial location of sampling across the study area but were affected by physicochemical changes associated with tillage induced soil homogenisation and plant presence. Tillage treatment effects on both species richness and composition were more evident for bacterial communities than fungal communities, and were greater at depths <15 cm. Homogenisation of soil and changing land management appears to redistribute both microbiota and nutrients deeper in the soil profile while consequences for soil biogeochemical functioning remain poorly understood.

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Continental-Scale Paddy Soil Bacterial Community Structure, Function and Biotic Interaction

10.21203/rs.3.rs-37103/v1 ◽

2020 ◽

Author(s):

Zhijian Zhang ◽

Hong-Yi Li ◽

Hang Wang ◽

Xing-Hua Tao ◽

Xian-Zhe Wang ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Environmental Factors ◽

Bacterial Community ◽

Paddy Soil ◽

Bacterial Community Structure ◽

Soil Bacteria ◽

Paddy Soils ◽

Continental Scale ◽

Soil Sustainability

Abstract Background: Rice paddy soil-associated microbiota participate in biogeochemical processes that underpin rice yield and soil sustainability, yet continental-scale biogeographic patterns of paddy soil microbiota remain elusive. Here, the soil bacteria of four typical Chinese rice-growing regions were characterized over large-scale space and compared with adjacent non-paddy soils.Results: The geographic patterns of paddy soil bacteria were significantly different from non-paddy soils, with lower alpha diversity, unique taxonomic and functional composition, and distinct co-occurrence network topology. Both stochastic and deterministic processes shaped soil bacteria assembly, but paddy exhibited a stronger deterministic signature than non-paddy samples, especially due to the roles of climate determinants. The continental biogeographic variance in bacterial community structure was driven by the competition between two mutually-exclusive bacterial modules in the co-occurrence network, and suggested antagonistic species-to-species interactions as potential selective forces may greatly shape their community structures. Keystone taxa identified in network models, such as Actinobacteria, Chloroflexi, and Proteobacteria, were demonstrated to be preferentially affected by environmental factors than other community members and showed high sensitivity to environmental changes, whereby the environmental factors greatly shaped the paddy soil bacterial communities by leveraging changes in keystones.Conclusions: The strong interplay between biotic/abiotic factors may greatly construct paddy soil microbial community and their uniqueness as compared with non-paddy soils. Microbial biogeographical analyses with novel insights into underlying determinants investigated on intensively-cultivated paddy field soils may aid in elucidating microbial changes subjected to land-use changes following the transformation between natural and agro-ecosystem, and also facilitate microbial community manipulation for better crop productivity and soil sustainability worldwide.

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Effects of Lactic Acid Bacterial Inoculants on Fermentation Quality, Bacterial Community, and Mycotoxins of Alfalfa Silage under Vacuum or Nonvacuum Treatment

Microorganisms ◽

10.3390/microorganisms9122614 ◽

2021 ◽

Vol 9 (12) ◽

pp. 2614

Author(s):

Xiaomiao Fan ◽

Shanshan Zhao ◽

Fengyuan Yang ◽

Yuan Wang ◽

Yanping Wang

Keyword(s):

Lactic Acid ◽

Microbial Community ◽

Bacterial Community ◽

High Throughput Sequencing ◽

Ammonia Nitrogen ◽

Positive Influence ◽

Bacterial Inoculants ◽

Fermentation Quality ◽

Alfalfa Silage ◽

Silage Quality

To investigate the effects of lactic acid bacterial (LAB) inoculants and vacuuming on the fermentation quality and bacterial community, alfalfas were ensiled with or without a commercial LAB YX or Lactobacillus plantarum strain ZZUA493 for 10, 30, 60, and 90 days while undergoing either vacuum (V) or nonvacuum (NV) treatment. At 90 days, analysis of the microbial community by high-throughput sequencing was performed, and contents of aflatoxin B1 and deoxynivalenol (DON) mycotoxins in alfalfa silage were determined. In all inoculated alfalfa silage, irrespective of V or NV treatment, lactic acid (LA) content increased, pH (p < 0.05), and ammonia nitrogen (p < 0.05) content decreased, and no butyric acid was detected. Lactobacillus or Pediococcus became the dominant genus, and the abundance of Garciella decreased in alfalfa silage with the addition of either inoculant. The LAB inoculants YX and ZZUA493 helped reduce the mycotoxin content in alfalfa silage. The abundance of Garciella in the control and DON content in all alfalfa silage groups were higher (p < 0.05) in NV than V. In summary, LAB inoculants and vacuuming had a positive influence on alfalfa silage quality, and LAB inoculants were effective in reducing mycotoxins in silage alfalfa.

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Biochar Suppresses Bacterial Wilt of Tomato by Improving Soil Chemical Properties and Shifting Soil Microbial Community

Microorganisms ◽

10.3390/microorganisms7120676 ◽

2019 ◽

Vol 7 (12) ◽

pp. 676 ◽

Cited By ~ 1

Author(s):

Yang Gao ◽

Yang Lu ◽

Weipeng Lin ◽

Jihui Tian ◽

Kunzheng Cai

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Bacterial Wilt ◽

Plant Disease Resistance ◽

Soil Microbial Community ◽

Chemical Properties ◽

Disease Suppression ◽

Soil Chemical Properties ◽

Soil Microbial ◽

Genus Level

The role of biochar amendments in enhancing plant disease resistance has been well documented, but its mechanism is not yet fully understood. In the present study, 2% biochar made from wheat straw was added to the soil of tomato infected by Ralstonia solanacearum to explore the interrelation among biochar, tomato bacterial wilt resistance, soil chemical properties, and soil microbial community and to decipher the disease suppression mechanisms from a soil microbial perspective. Biochar application significantly reduced the disease severity of bacterial wilt, increased soil total organic carbon, total nitrogen, C:N ratio, organic matter, available P, available K, pH, and electrical conductivity. Biochar treatment also increased soil acid phosphatase activity under the non-R.-solanacearum-inoculated condition. High-throughput sequencing of 16S rRNA revealed substantial differences in rhizosphere bacterial community structures between biochar-amended and nonamended treatments. Biochar did not influence soil microbial richness and diversity but significantly increased the relative abundance of Bacteroidetes and Proteobacteria in soil at the phylum level under R. solanacearum inoculation. Furthermore, biochar amendment harbored a higher abundance of Chitinophaga, Flavitalea, Adhaeribacter, Pontibacter, Pedobacter, and Ohtaekwangia at the genus level of Bacteroides and Pseudomonas at the genus level of Proteobacteria under R. solanacearum inoculation. Our findings suggest that a biochar-shifted soil bacterial community structure can favorably contribute to the resistance of tomato plants against bacterial wilt.

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Organic Amendments and Sampling Date Influences on Soil Bacterial Community Composition and Their PredictiveFunctional Profiles in an Olive Grove Ecosystem

Agriculture ◽

10.3390/agriculture11111178 ◽

2021 ◽

Vol 11 (11) ◽

pp. 1178

Author(s):

Laura L. de Sosa ◽

Beatriz Moreno ◽

Rafael Alcalá Alcalá Herrera ◽

Marco Panettieri ◽

Engracia Madejón ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Agricultural Soils ◽

Soil Microbial Communities ◽

Soil Bacterial Community ◽

Olive Grove ◽

Soil Microbial Diversity ◽

Soil Microbial ◽

Soil Bacterial ◽

The Impact

A collapse of soil microbial diversity, mainly due to chemical inputs, has been reported to lead to the degradation of conventional agroecosystems. The use of compost from urban and agricultural waste management, in order to achieve a net gain in the storage of C, is an adequate management of agricultural soils, especially in rainfed conditions. However, the great variability of composts of different maturity and origins and of the soils to which they are added limits the ability to predict the impact of these amendments on the dynamics of soil microbial communities. This study was designed to gain insights on the effect of exogenous organic matter management on the soil bacterial community and its contribution to key functions relevant to agricultural soils. To achieve this, two different types of compost (alperujo or biosolids composts) at two doses were used as soil amendments twice for 3 years in a rainfed olive grove ecosystem. A metagenomic analysis was carried out to assess the abundance and composition of the soil bacterial communities and predicted functions. We only detected a minor and transitory effect on the bacterial abundance of the soil, the structure of the community and the potential functions, less related to the dose or the type of compost than to seasonal variations. Although the result suggests that the soil bacteria were highly resilient, promoting community stability and functional resilience after the addition of the two composts, more efforts are necessary to assess not only the resulting soil microbial community after organic fertilization but the intrinsic microbial community within the organic amendment that acts as an inoculum, and to what extent the changes in its dose could lead to the functionality of the soil.

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Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils

10.7287/peerj.preprints.3288 ◽

2017 ◽

Author(s):

Craig Anderson ◽

Mike Beare ◽

Hannah L Buckley ◽

Gavin Lear

Keyword(s):

Microbial Community ◽

Agricultural Soils ◽

Microbial Community Composition ◽

Chemical Properties ◽

Community Response ◽

Fungal Communities ◽

Physicochemical Changes ◽

Tillage Depth ◽

Tillage Treatment

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Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils

PeerJ ◽

10.7717/peerj.3930 ◽

2017 ◽

Vol 5 ◽

pp. e3930 ◽

Cited By ~ 11

Author(s):

Craig Anderson ◽

Mike Beare ◽

Hannah L. Buckley ◽

Gavin Lear

Keyword(s):

Microbial Community ◽

Agricultural Soils ◽

Microbial Community Composition ◽

Chemical Properties ◽

Community Response ◽

Fungal Communities ◽

Physicochemical Changes ◽

Tillage Depth ◽

Tillage Treatment

In arable cropping systems, reduced or conservation tillage practices are linked with improved soil quality, C retention and higher microbial biomass, but most long-term studies rarely focus on depths greater than 15 cm nor allow comparison of microbial community responses to agricultural practices. We investigated microbial community structure in a long-term field trial (12-years, Lincoln, New Zealand) established in a silt-loam soil over four depth ranges down to 30 cm. Our objectives were to investigate the degree of homogenisation of soil biological and chemical properties with depth, and to determine the main drivers of microbial community response to tillage. We hypothesised that soil microbiological responses would depend on tillage depth, observed by a homogenisation of microbial community composition within the tilled zone. Tillage treatments were mouldboard plough and disc harrow, impacting soil to ∼20 and ∼10 cm depth, respectively. These treatments were compared to a no-tillage treatment and two control treatments, both permanent pasture and permanent fallow. Bacterial and fungal communities collected from the site were not impacted by the spatial location of sampling across the study area but were affected by physicochemical changes associated with tillage induced soil homogenisation and plant presence. Tillage treatment effects on both species richness and composition were more evident for bacterial communities than fungal communities, and were greater at depths <15 cm. Homogenisation of soil and changing land management appears to redistribute both microbiota and nutrients deeper in the soil profile while consequences for soil biogeochemical functioning remain poorly understood.

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