Community In Paddy Soil Research Articles

Impact of Methanotrophic and N2O-reducing Bacterial Inoculation on CH4 and N2O Emissions, Paddy Growth and Bacterial Community Structure in Paddy Field

Paddy field is one of the anthropogenic sources that produce greenhouse gases emission. This study aimed to investigate the impact of methanotrophic and N2O-reducing bacterial inoculation on CH4 and N2O emissions, paddy growth and bacterial community structure in paddy field. Two treatments of 100% synthetic fertilizer (250 kg urea/ha) without biofertilizer and 50% synthetic fertilizer (125 kg urea/ha) with biofertilizer consisted of methanotrophic and N2O-reducing bacteria were applied in the paddy field. Inoculation of methanotrophic and N2O-reducing bacteria was able to reduce CH4 and N2O emission up to 4.19 mg CH4/m2/day and 351.29 µg N2O/m2/day, respectively. Those bacterial applications were also able to increase paddy growth and yield productivity. According to DGGE profile, inoculation of the biofertilizer seemed to have a transient impact on bacterial communities in paddy soil at 36 days after transplanting (DAT) which showed the lowest similarity with all samples (a similarity index of 0.68). DGGE bands successfully excised have closest relative to uncultured bacteria which comprised 5 phyla, i.e. Proteobacteria (Alphaproteobacteria and Deltaproteobacteria), Nitrospirae, Actinobacteria, Firmicutes, and Acidobacteria. In this study, Alphaproteobacteria was the most dominant phylum. We provide basic information for developing the biofertilizer which supports sustainable agriculture.

The response of arsenic bioavailability and microbial community in paddy soil with the application of sulfur fertilizers

Arsenic (As) has been recognized as one of the most toxic metalloids present in the surface soil contaminating food chain and posing threat to human life. Sulfur (S) fertilizer is often supplied in paddy soil for rice growth, but its impact on As mobility and related bacteria remains poorly understood. In this study, a pot experiment was set up with two different types of sulfur treatments (element sulfur and Na2SO4) to evaluate the effect of sulfur fertilizers on As speciation in porewater, As fractions in soil, As accumulation in rice plants. Besides, rhizosphere bacterial composition and functional genes that might influence As mobility were also studied. The results revealed that the addition of 150 mg/kg Na2SO4 decreased As(III) and As(V) concentrations in soil porewater at maturation stage by 77% and 64%, respectively. With the same sulfur content, Na2SO4 was more effective than element sulfur. The addition of sulfur fertilizers promoted rice growth and reduced As accumulation in shoots, further reduced As translocation from root to above-ground parts by 39–59%. The addition of sulfur fertilizers had little effect on genes involved in As metabolism. However, the relative abundance of Fe(III) and sulfate reduction related genera increased with the addition of 150 mg/kg Na2SO4, consistent with the increase of Fe(III) reducing bacteria Geobacteraceae and sulfate reducing gene dsrA. The phenomenon likely influenced the decrease of As concentrations in soil porewater and rice uptake. The outcomes indicate that promoting Fe- and S- reducing bacteria in the rhizosphere by sulfur fertilizers may be one way to reduce As risk in the soil-rice system.

Abundance, diversity, and structure of Geobacteraceae community in paddy soil under long-term fertilization practices

Geobacteraceae is an important dissimilatory Fe(III) reducer that affects the cycles of multiple elements. However, the way in which different long-term fertilization regimes influence the Geobacteraceae community in paddy soils remains unknown. Therefore, the objective of this study was to explore the responses of Geobacteraceae community in paddy soil to long-term chemical (nitrogen, phosphorus, and potassium) and/or organic (manure) fertilization practices. Illumina sequencing results showed that the species richness and diversity of Geobacteraceae community were not significantly changed by fertilizer treatments. Geobacteraceae in the treatments consisted of Geobacter (accounting for 90%–95% of total reads) and Geothermobacter genera (5%–10%), and all fertilizer treatments induced a significant (P < 0.05) decline in Geobacter and a marked enrichment of Geothermobacter. The taxonomic (based on Bray-Curtis distance) and phylogenetic structures (weighted-UniFrac distance) of the Geobacteraceae communities in all fertilizer treatments were clearly different from those in the non-fertilizer treatment; however, there were no significant changes among the different fertilization treatments. The variations in the Geobacteraceae community induced by long-term fertilization were mainly determined by changes in soil pH, total carbon, and total nitrogen. These findings provide an insight into the biogeochemistry of paddy soils and pave the way for harnessing the microbiome to improve soil fertility and environmental quality.

Ecological drivers of methanotrophic communities in paddy soils around mercury mining areas

Methanotrophs play a crucial role in mitigating methane (CH4) emission by oxidizing produced CH4 in paddy soils; however, ecological drivers of methanotrophic community in the soils around heavy metal contaminated areas remain unclear. In this study, we evaluated the effects of heavy metal pollution and soil properties on the abundance, diversity and composition of methanotrophic community in paddy soils from two typical mercury (Hg) mining regions in southwest China. The results of random forest and structure equation models suggest that both heavy metal content and soil nutrients greatly influenced the attributes of methanotrophic community. In general, the abundance and diversity of methanotrophs were negatively related to soil Hg content, but showed positive correlation with soil organic carbon content. However, the other metals (cadmium (Cd), nickel (Ni), lead (Pb), arsenic (As), zinc (Zn)) had inconsistent associations with the microbial indexes of methanotrophic community in the soil. Elevated levels of heavy metal and nutrients in the soils shifted the community composition of methanotrophs. For example, Pb, As and Zn contents had negative associations with the relative abundance of Methylocaldum. In addition, changes in the relative abundance of ecological clusters within the co-occurrence network of methanotrophs were related to metal contents and soil properties. Together, our findings provide novel insights into understanding ecological drivers of methanotrophic community in paddy soils around Hg mining regions, with important implications for mitigating CH4 emissions in terrestrial ecosystems.

Shifts in short-chain fatty acid profile, Fe(III) reduction and bacterial community with biochar amendment in rice paddy soil.

Biochar, a valuable product from the pyrolysis of agricultural and forestry residues, has been widely applied as soil amendment. However, the effect of different types of biochar on soil microorganisms and associated biochemical processes in paddy soil remains ambiguous. In this study, we investigated the impact of biochars derived from different feedstocks (rice straw, orange peel and bamboo powder) on the dynamics of short-chain fatty acids (SCFAs), iron concentration and bacterial community in paddy soil within 90 days of anaerobic incubation. Results showed that biochar amendment overall inhibited the accumulation of SCFAs while accelerating the Fe(III) reduction process in paddy soil. In addition, 16S rRNA gene sequencing results demonstrated that the α-diversity of the bacterial community significantly decreased in response to biochar amendments at day 1 but was relatively unaffected at the end of incubation, and incubation time was the major driver for the succession of the bacterial community. Furthermore, significant correlations between parameters (e.g. SCFAs and iron concentration) and bacterial taxa (e.g. Clostridia, Syntrophus, Syntrophobacter and Desulfatiglans) were observed. Overall, our findings demonstrated amendment with different types of biochar altered SCFA profile, Fe(III) reduction and bacterial biodiversity in rice paddy soil.

Distribution characteristics of fungal communities with depth in paddy fields of three soil types in China.

Little is known about the distribution of fungal communities with soil depth on relatively large scales. In this study, typical paddy soils in three regions (Hailun, Changshu, and Yingtan) from north to south China were selected to investigate the vertical distribution (0-100 cm) of the fungal community by Illumina MiSeq sequencing, and to identify the main factors influencing the fungal community distribution. The results indicated that the structure of the soil fungal community changed significantly with region and soil depth. Soil fungal taxa such as Zygomycota, Glomeromycota, Saccharomycete, Kazachstania, Mortierella, Massariosphaeria, Hypholoma, and Zopfiella were enriched at depths of 0-20 cm, whereas Dothideomycetes, Microbotryomycetes, Tremellomycetes, Sporobolomyces, Cryptococcus, Rhodotorula, Fusarium, and Pyrenochaetopsis had high relative abundances at 80-100 cm. Variance partitioning analysis indicated that the geographic distance contributed more to the fungal community variation than environmental variables on a large scale. In addition, soil total carbon and nitrogen contents were the main environmental factors driving the vertical distribution of the fungal community in paddy soils.

Co‐incorporation of Chinese milk vetch (Astragalus sinicus L.) and rice (Oryza sativa L.) straw minimizes CH4 emissions by changing the methanogenic and methanotrophic communities in a paddy soil

AbstractThe practice of co‐incorporating rice straw and leguminous green manure (such as Chinese milk vetch) into paddy soils has become increasingly popular in the last 10 years, although its effect on soil CH4 emissions and microbial community structure is poorly understood. In this study, data from a 2‐year pot experiment were used to reveal the effects of the co‐incorporation of rice straw and Chinese milk vetch on CH4 emissions and methanogenic and methanotrophic communities in paddy soil. Five treatments were chosen: CK (unamended control), CF (inorganic fertilizer), FM (inorganic fertilizer and Chinese milk vetch, 20 g 10 kg−1 dry soil, 4.5 t ha−1), FR (inorganic fertilizer and rice straw, 20 g 10 kg−1 dry soil, 4.5 t ha−1) and FMR (inorganic fertilizer and Chinese milk vetch and rice straw mixture, 5 + 15 g 10 kg−1 dry soil, 1.125 + 2.375 t ha−1). Overall, the soil CH4 emissions in the 2 years under all residue treatments (104.4–122.8 and 83.3–133.3 g CH4 m−2) were higher than those in CK (57.0 and 20.7 g CH4 m−2) and CF (71.8 and 21.9 g CH4 m−2) treatments. The FMR treatment decreased CH4 emissions when compared with FM and FR, especially in the second year. A higher abundance of methanogens (mcrA gene copies) was found under the plant residue‐treated soils (4.35 × 108 g−1 dry soil on average) and FM increased the abundance of methanotrophs (pmoA gene copies, 2.68 × 106 g−1 dry soil). Application of plant residues changed the methanogenic and methanotrophic community structures in comparison with CF (e.g., markedly increased the populations of Methanobacteriales and Methylomonas and suppressed Methanomicrobiales and Methylobacter populations). Methane emissions were significantly and positively related to the mcrA and pmoA gene copy numbers, as well as the mcrA/pmoA ratio. The partial least squares path model (PLS‐PM) indicated that the rice plant biomass (path coefficient = 0.64), the abundance of methanogens (path coefficient = 0.57) and the community structure of methanotrophs (path coefficient = −0.59) were determinants of CH4 emissions. Among the three residue‐treated soils, FMR showed the lowest CH4 emissions and was associated with a slight decrease in the mcrA/pmoA ratio and a significant increase in the Type I/Type II methanotrophs ratio. Thus, we recommend the co‐incorporation of Chinese milk vetch and rice straw as a sustainable fertilization pattern to improve the growth of rice and minimize CH4 emissions.Highlights Residue application improves rice productivity (except for FR), soil fertility and CH4 emissions. Co‐incorporation of MV and RS reduces CH4 emissions in comparison with pure MV or RS addition. Residue application changes the community structure of methanogens and methanotrophs. The methanogenic abundance and the methanotrophic community structure determine the CH4 emissions.

Flooding Irrigation Weakens the Molecular Ecological Network Complexity of Soil Microbes During the Process of Dryland-to-Paddy Conversion.

Irrigation has been applied on a large scale for the improvement of grain yield per hectare and production stability. However, the dryland-to-paddy conversion affects the ecological environment of areas of long-term dry farming, especially soil microorganisms. Little attention has been paid to the changes in microbial communities and the interactions between their populations in this process. Therefore, in this paper, the compositions and diversity of soil bacterial and fungal communities were explored through a combination of high-throughput sequencing technology and molecular ecological network methods using bacterial 16S rRNA and fungal ITS. The results showed that: (1) both the abundance and diversity of soil bacteria and fungi decreased in a short time, and the abundance of Actinobacteria, Firmicutes and Olpidiomycota varied greatly. (2) Compared to dry land, the modular structure of interaction networks and interspecific relationships of bacterial and fungal communities in paddy soil were simpler, and the network became more unstable. A cooperative relationship dominated in the molecular ecological network of bacteria, while a competitive relationship was dominant in the network of fungi. Actinobacteria and Firmicutes were the dominant bacterial species in dry land and paddy field, respectively. Ascomycota was dominant in the fungal communities of both dry land and paddy field. (3) The change in soil environmental factors, such as pH, electrical conductivity (EC), organic matter (OM) and available potassium (AK), directly affected the soil microbial community structure, showing a significant correlation (p < 0.05). These environmental factors also influenced the dominant microbial species. Microorganisms are the most important link in the carbon and nitrogen cycles of soil, and a large-scale dryland-to-paddy conversion may reduce the ecological stability of regional soil.

Acetotrophic methanogens are sensitive to long-term nickel contamination in paddy soil.

Paddy soil accounts for approximately one-fifth of the world's cultivated area and faces a serious threat from nickel (Ni). Ni pollution has an impact on the activity, composition and emission of methanogens in paddy, which is a major natural source of methane (CH4) emissions. We combined a high-throughput sequencing approach and laboratory incubation methods to evaluate the impact of long-term Ni pollution on the methanogenic archaeal community in paddy soil. The highest rate of CH4 production was 697 mg kg-1 of dry soil per d with the addition of sodium acetate at 50 mg kg-1 of Ni, which was significantly negatively correlated with the total and available Ni (p < 0.05). While the highest CH4 production rates were 485 and 544 mg kg-1 of dry soil per d with the addition of sodium formate and methanol, respectively, there was no significant difference in the CH4 production rate and maximum CH4 accumulation between the different Ni additions. Heavy pollution with 500 mg kg-1 of Ni unexceptionally inhibited the relative abundance of various genera of methanogens (22.2% in total). The abundance of acetotrophic Methanosaeta decreased with an increasing concentration of Ni (3.25-1.11%). The diverse nutrient types of species belonging to Methanosarcina were the highest under treatment with Ni200 (18.0%), and lowest in the soil with 500 mg kg-1 of Ni (2.8%). Similarly, the abundances of the most abundant hydrogenotrophic methanogens of Methanocellales were relatively high with Ni200 (26.2%) compared with those with Ni500 (5.4%). The mcrA gene was enriched under the light pollution treatment (50 mg kg-1 of Ni, 6.73 × 107 ± 9.0 × 106 copies per g of soil) compared with the control (4.18 × 107 ± 5.1 × 106 copies per g of soil). These results indicate that the long-term pollution by Ni has an impact on the activity and composition of methanogens with heavy Ni pollution, and in particular, acetotrophic methanogens are sensitive to Ni pollution in paddy soil.

Variation in soil bacterial communities by long-term application of organic and inorganic fertilizers in rice

Fertilization plays important role in increasing the quality of soil and crop productivity. Soil bacterial communities are sensitive indicators of soil quality and their response to long-term fertilization in paddy soils of Kerala remains unexplored. In the present study, we analysed the long term effect of fertilizer regimes viz., organic inputs (ONM), integrated inputs (INM) and inorganic (INF) inputs on bacterial community in paddy soils using NGS sequencing of 16S rRNA genes. The results showed that relative abundance of bacterial communities varied across organic and inorganic fertilizer treatments. The dominant phyla across all the treatments were Actinobacteria followed by Acidobacteria, Proteobacteria and Firmicutes. The long term application of organic and integrated fertilizers clearly increased the abundance of beneficial microbes like Bacillus, Arthrobacter, Bradyrhizobium, Frankia etc in soil. In contrast, continuous use of chemical fertilizers, suppressed the growth of Rhizobium, Azospirillum, Pseudomonas and Burkholderia in rhizosphere soils. Overall, the present study enhanced our understanding of relationship between soil microbiota and functioning of agro ecosystem and support the use of integrated fertilization strategy in rice. DOI: https://doi.org/10.25174/2249-4065/2019/94878

Non-target effect of bispyribac sodium on soil microbial community in paddy soil.

Bispyribac sodium is frequently used herbicide in the rice field. Though, it has been targeted to kill rice weeds, but its non-target effect on soil microbes in paddy soil was largely unknown. Therefore, in the present study, an attempt was made to assess the non-target effect of bispyribac sodium on alteration of functional variation of soil microbial community and their correlation with microbial biomass carbon (MBC) and soil enzymes. A microcosm experiment set up was made comprising three treatments viz., control (CON) (without application of bispyribac sodium), recommended dose of bispyribac sodium (35gha-1) (BS), and double the dose of BS (70gha-1) (DBS). Results indicated that the MBC and soil enzyme activities (dehydrogenase, alkaline phosphatase and urease) in BS and DBS-treated soil were significantly (p<0.05) declined from 1st to 30th day after application as compared to CON. Counts of heterotrophic bacteria, actinomycetes and fungal population were also decreased in BS and DBS-treated soil. The average well color development (AWCD) values derived from Biolog®ecoplates followed the order of DBS ˂ BS ˂ CON. Shannon index value was high (p≤0.05) in CON compared to soil-treated with BS and DBS. Principal component analysis (PCA) showed a clear distinction of the cluster of treatments between CON, BS and DBS. Biplot analysis and heatmap suggested that carboxylic compounds and amino acids showed positive response towards BS-treated soil, whereas phenolic compounds had positive correlation with DBS-treated soil. PCA analysis indicated that oligotrophs was rich in BS-treated paddy soil, whereas copiotrophs and asymbiotic nitrogen fixers were richer in DBS treatment. Overall, the present study revealed that application of recommended dose of BS and its double dose alter the soil microbial population, enzyme activities and functional microbial diversity in paddy soil.

Shifts in bacterial community composition increase with depth in three soil types from paddy fields in China

Bacterial community distribution along soil depth gradients is currently poorly understood at the large scale. We selected three typical paddy soils in three regions from north to south in China to investigate the vertical distribution (0–100 cm) of the bacterial community by Illumina MiSeq amplicon sequencing and identify its drivers. Results indicated that the dominant bacterial phyla in paddy soils were Chloroflexi, Acidobacteria, and Proteobacteria. The four diversity indices of the bacterial community all increased at depths of 0–20 cm, then gradually decreased at depths of 20–100 cm. Linear discriminant analysis effect size showed that some bacterial taxa displayed significant differences in relative abundance among different depth gradients. Some bacterial taxa (such as phyla Chloroflexi, Bacteroidetes, and Nitrospirae; classes Alphaproteobacteria, Betaproteobacteria, and Anaerolineae; and genera Candidatus Koribacter and Rhodoplanes) had a high relative abundance at depths of 0–20 cm. Other taxa (belonging to classes Deltaproteobacteria and Gammaproteobacteria and to genera Geobacter and Acinetobacter) had a high relative abundance at depths of 80–100 cm. Non-metric multidimensional scaling analysis indicated that the soil bacterial community structure clearly changed with region and soil depth, and the shifts in bacterial community composition increased with depth in three paddy soils. Variance partitioning analysis showed that geographic distance had more effect on bacterial community distribution than environmental variables in deeper soil (20–100 cm) at a large scale. In addition, distance-based redundancy analysis suggested that soil total carbon and nitrogen contents were strongly associated with the vertical distribution of the bacterial community in paddy soil.

High-throughput sequencing analysis of microbial community diversity in response to indica and japonica bar-transgenic rice paddy soils.

Potential environmental risks of genetically modified (GM) crops have raised concerns. To better understand the effect of transgenic rice on the bacterial community in paddy soil, a field experiment was carried out using pairs of rice varieties from two subspecies (indica and japonica) containing bar transgene with herbicide resistance and their parental conventional rice. The 16S rRNA gene of soil genomic DNA from different soil layers at the maturity stage was sequenced using high-throughput sequencing on the Illumina MiSeq platform to explore the microbial community diversity among different rice soils. There were no significant differences in diversity indices between transgenic japonica rice and its sister conventional rice (japonica pair) among different soil layers, but, significant differences was observed between transgenic indica rice and its conventional rice (indica pair) in the topsoil layer around concentrated rice roots according to the ace diversity index. Though the japonica rice soil and indica rice soil were shared several key genera, including Rivibacter, Anaeromyxobacter, Roseomonas, Geobacter, Thiobacillus, Clostridium, and Desulfobulbus, the primary bacterial genera in indica rice soil were different from those in japonica rice. Synechococcus and Dechloromonas were present in japonica rice samples, while Chloronema, Flexibacter, and Blastocatella were observed in indica rice soil. Moreover, the abundance of genera between GM and non-GM varieties in japonica rice was significantly different from indica rice, and several bacterial communities influenced these differences. Anaerovorax was more abundant in transgenic japonica rice soil than conventional rice soil, while it was deficient in transgenic indica rice soil compared to conventional rice soil, and opposite responses to Deferrisoma were in that of indica rice. Thus, we concluded that transgenic indica and japonica rice had different effects on soil bacteria compared with their corresponding sister conventional rice. However, these composition and abundance difference only occurred for a few genera but had no effect on the primary genera and soil characteristics were mainly contributed to these differences. Thus, differences in bacterial community structure can be ignored when evaluating the impacts of transgenic rice in the complex soil microenvironment.

Influence of elevated CO2 on arbuscular mycorrhizal fungal community elucidated using Illumina MiSeq platform in sub-humid tropical paddy soil

Arbuscular mycorrhizal fungi (AMF) are one of the beneficial soil microbial communities, playing an important role in abiotic and biotic stress management in agricultural crops, including rice. Climate change, particularly elevated CO2 (eCO2) alters the soil microbial community, but the alteration of AMF community has received little attention, partly because of inadequacy in understanding of AMF taxonomy. Therefore, an attempt was made to understand AMF community in paddy soil under long-term exposure (8 years) to eCO2 through sequencing 18S rRNA small subunit SSU based Illumina Miseq technique using the primer pair AML1/AML2. Changes in OTUs belonging to 23 AMF species were identified in the ambient (400 ± 10 μmol mol−1) and eCO2 (550 ± 20 μmol mol−1) conditions, respectively based on reads alignment using MaarjAM VT database. Moreover, principal coordinate (PCO) analysis clustered the related OTUs and suggested that long-term exposure of eCO2 suppressed the OTUs of Glomerales and encouraged the OTUs of Diversisporales. Overall, the present study indicates that long-term exposure of paddy soil to eCO2 (550 ppm) drastically reduced the commonly occuring AMF such as Claroideoglomus and Glomus species in sub-humid tropical condition.

Identification of potential electrotrophic microbial community in paddy soils by enrichment of microbial electrolysis cell biocathodes

Electrotrophs are microbes that can receive electrons directly from cathode in a microbial electrolysis cell (MEC). They not only participate in organic biosynthesis, but also be crucial in cathode-based bioremediation. However, little is known about the electrotrophic community in paddy soils. Here, the putative electrotrophs were enriched by cathodes of MECs constructed from five paddy soils with various properties using bicarbonate as an electron acceptor, and identified by 16S rRNA-gene based Illumina sequencing. The electrons were gradually consumed on the cathodes, and 25%–45% of which were recovered to reduce bicarbonate to acetic acid during MEC operation. Firmicutes was the dominant bacterial phylum on the cathodes, and Bacillus genus within this phylum was greatly enriched and was the most abundant population among the detected putative electrotrophs for almost all soils. Furthermore, several other members of Firmicutes and Proteobacteria may also participate in electrotrophic process in different soils. Soil pH, amorphous iron and electrical conductivity significantly influenced the putative electrotrophic bacterial community, which explained about 33.5% of the community structural variation. This study provides a basis for understanding the microbial diversity of putative electrotrophs in paddy soils, and highlights the importance of soil properties in shaping the community of putative electrotrophs.

Rice Rotation System Affects the Spatial Dynamics of the Diazotrophic Community in Paddy Soil of the Yangtze Delta, China

Rice-wheat (RW), rice-fallow (RF), and rice-Chinese milk vetch (RM) are the three major rice rotation systems currently used in the Yangtze Delta of China. However, it remains poorly understood how these systems affect microbial communities in soils. Quantitative polymerase chain reaction (qPCR) and denaturing gradient gel electrophoresis (DGGE) were used to analyze the composition, abundance and diversity of diazotrophic community at different depths in soils under RW, RF and RM treatments. The results showed that rice yields were significantly higher in RM as compared to those in RF and RW in all years from 2011 to 2016. Diazotrophic communities at soil depths of 10–20 cm and 40–80 cm under RM were significantly more diverse than those under the other treatments. Sequences affiliated with Geoalkalibacter spp. showed the greatest abundance under RW at all soil depths, while Desulfovibrio and Pseudacidovorax spp. were both more abundant under RM at the 40–80 cm depth. Redundancy analysis (RDA) identified that the diazotrophic community within the 40–80 cm layer of soil under RM was positively associated with soil macro-aggregates. In conclusion, the RM treatment was characterized by significantly higher diversity of diazotrophic community in subsoil and increased rice yields as compared to the other treatments.

Paddy System with a Hybrid Rice Enhances Cyanobacteria Nostoc and Increases N2 Fixation

Biological nitrogen (N) fixation (BNF) plays a significant role in maintaining soil fertility in paddy field ecosystems. Rice variety influences BNF, but how different rice varieties regulate BNF and associated diazotroph communities has not been quantified. Airtight, field-based 15N2-labelling growth chamber experiments were used to assess the BNF capacity of different rice varieties. In addition, both the 16S rRNA and nifH genes were sequenced to assess the influence of different rice varieties on bacterial and diazotrophic communities in paddy soils. After subjecting a rice-soil system to 74 d of continuous airtight, field-based 15N2 labelling in pots in a growth chamber, the amounts of fixed N were 22.3 and 38.9 kg ha–1 in inbred japonica (W23) and hybrid indica (IIY) rice cultivars planted in the rice-soil systems, respectively, and only 1%–2.5% of the fixed N was allocated to the rice plants and weeds. A greater abundance of diazotrophs was found in the surface soil (0–1 cm) under IIY than under W23. Sequencing of the 16S rRNA gene showed significantly greater abundances of the cyanobacterial genera Nostoc, Anabaena, and Cylindrospermum under IIY than under W23. Sequencing of the nifH gene also showed a significantly greater abundance of Nostoc under IIY than under W23. These results indicate that the hybrid rice cultivar (IIY) promoted BNF to a greater extent than the inbred rice cultivar (W23) and that the increase in BNF might have been due to the enhanced heterocystous cyanobacteria Nostoc.

Dynamics of Bacterial and Viral Communities in Paddy Soil with Irrigation and Urea Application.

Viruses are ubiquitous in natural systems. By influencing bacterial abundance (BA) and community structure through lysis-lysogenic conversion, viruses are involved in various ecological processes. In agricultural management, nitrogen addition and irrigation should be considered as important factors that can modify soil viral dynamics but have been ignored. In our study, short-term dynamics of autochthonous soil viral and bacterial abundance and diversity after irrigation and urea application were examined in a long-term experimental paddy field. Urea addition delayed the emergence of peak viral abundance for three days, suggesting that viruses are sensitive to N addition. Under short-term eutrophic conditions through urea application, viruses undertake a lysogenic-biased strategy. Moreover, nitrogen-fixing bacteria were most likely specifically lysed in urea-treated soil, which suggests that soil viruses block N accumulation by killing nitrogen-fixing bacteria. To the best of our knowledge, this study is the first to investigate dynamic changes in autochthonous viruses in paddy fields.

Application of biodegradable seedling trays in paddy fields: Impacts on the microbial community

Biodegradable plastics have been widely introduced into agricultural production, but their impacts on the soil ecosystem remain unclear. The present study investigated the impacts of a biodegradable seedling tray (BST) on the microbial communities in paddy soils. A 110-day rice culture experiment was conducted with three different paddy soils developed from black soil (BS, black chernozem soil), chao soil (CS, Fluvo-aquic) and red soil (RS, Alfisols) and three application rates of BST (0, 0.02 and 0.2 g kg−1). Soil phthalic acid ester (PAE) concentrations, physicochemical properties and enzyme activities were determined to evaluate the influence of BSTs on soil quality. 16S high-throughput sequencing was used to study bacterial community composition and the Biolog EcoPlate™ test was used to profile microbial activity and community function. Results show that the application of BSTs did not markedly affect soil quality, and the potential release of PAEs from BSTs was negligible. Interestingly, the microbial community was affected by BSTs in a soil-dependent and time-dependent pattern. The microbial community in RS was not significantly influenced by BSTs. Relative abundances of some predominant genera in BS (e.g. norank_f__BSV40) and CS (e.g. Norank_f__Nitrosomonadaceae) were significantly influenced by BSTs, and db-RDA results show that community composition in BS and CS was shaped mainly by BSTs. Community level profiling shows that BSTs significantly increased microbial activity and decreased functional diversity in BS after 55 days, but the impacts disappeared after 110 days. The results contribute to the knowledge of how biodegradable plastics influence microbial communities in paddy fields and provide information relevant to the practical use of BSTs under field condition.

Bacterial community variations in paddy soils induced by application of veterinary antibiotics in plant-soil systems

Soil bacterial communities have complex regulatory networks, which are mainly associated with soil fertility and ecological functions, and are likely to be disturbed due to antibiotics applications. The impact of antibiotics, particularly in mixtures form, on bacterial communities in different paddy soils is poorly understood. Using pyrosequencing techniques of 16 S rRNA genes, this study investigated the synergistic effects of veterinary antibiotics (sulfadiazine, sulfamethoxazole, trimethoprim, florfenicol, and clarithromycin) on bacterial communities in a soil-bacteria-plant system. Rice was grown under controlled greenhouse conditions where unplanted and planted treatments were doped with 200 µg kg−1 of combined antibiotics over a period of 3 months. Bacterial richness remained unaltered, while a significant decline was observed in bacterial diversity due to antibiotics in the four paddy soils. Bacteroidetes and Acidobacteria were increased, while Actinobacteria and Firmicutes decreased under antibiotics exposure. Despite antibiotics perturbation, compositional variations were mainly attributed to the different paddy soils which harbor distinct bacterial communities. Haliangium and Gaiella were among the sensitive genera that were negatively correlated to antibiotics perturbation. Additionally, electrical conductivity, total organic carbon, and total nitrogen of soil solution were the key physiochemical indices which significantly influenced the structure of bacterial communities in the paddy soils. These findings expanded our knowledge of effects from synergistic antibiotics application and variations in bacterial communities among different paddy soils.