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Replanting disease is a growing problem in intensive agricultural systems. Application of bio-fertilizer containing beneficial microbes contributes to disease suppression and is a promising strategy to control replanting disease. However, the effect of both replanting disease and bio-fertilizer amendment on the assembly of crop microbiota in leaves and roots and their relationships to crop yield and quality remains elusive. In these experiments, roots and leaves of Radix pseudostellariae were collected from different consecutive monoculture and bio-fertilizer amended fields, and the associated microbiota were characterized by bacterial 16S rRNA gene sequencing and quantitative PCR. Consecutive monoculture altered the bacterial community structure and composition and significantly increased the abundance of potential pathogenic Ralstonia and Fusarium oxysporum in leaves and roots. Furthermore, bio-fertilizer application alleviated replanting disease by decreasing the pathogen load, increasing the potential beneficial genera Pseudomonas, Streptomyces, Paenibacillus, and Bradyrhizobium. The proportion of positive correlations in the co-occurrence network of bio-fertilizer application was the highest, implying that bio-fertilizer potentially enhanced ecological commensalism or mutualism of the bacterial community across the two compartments. Structural equation models indicated that bio-fertilizer had a positive and indirect effect on both yield and quality by shaping the leaf microbiota and the root microbiota. Our findings highlight the role of leaf and root microbiota on replanting disease, showing that bio-fertilizer contributes to alleviating replanting disease by improving microbe-microbe interactions.

The consecutive monoculture ofIn the present research, a continuous cropping facilitatorThe results showed that the land equivalent ratio (LER) of the two years was 1.17, and the system productivity index (SPI) increased by 16.92 % under S treatment, whereas no significant difference was found in N and M regimes. In the rhizosphere soil, intercropping systems had significantly increased the contents of sugars and malic acid in the soil ofTaken together, our study indicated that the

Traditional agricultural systems increasingly contribute to food and livelihood security worldwide. Previous studies have demonstrated the positive effects of intercropping on crop productivity due to the reduced impact of disease. However, surprisingly few studies to date have explored the mechanisms underlying the alleviation of agricultural replanting disease by intraspecific intercropping. Here, we performed metabolomic, high-throughput sequencing and quantitative PCR analysis to explore the beneficial effects of intraspecific intercropping on Radix pseudostellariae yields, soil metabolite abundance and microbial communities. Our results showed that intraspecific intercropping alleviated the serious replanting disease of R. pseudostellariae. The intercropping increased fungal and bacterial community diversity, increasing the relative abundances of potentially beneficial taxa (e.g., Nitrosomonadales, Nitrospirales, and Pseudomonadales), and decreasing the relative abundances of pathogenic taxa (e.g., Aspergillus and Talaromyces). Quantitative PCR analysis showed intercropping significantly decreased the populations of pathogenic F. oxysporum, and increased the beneficial Pseudomonas spp. and Burkholderia spp. as compared to monoculture. Our findings also suggested that intraspecific intercropping tightened associations within the soil microbiome and promoted microbial co-occurrence. Specifically, we observed that soils subjected to the consecutive monoculture of two plant varieties contained fewer metabolites, while intercropping increased the abundances of metabolites in the second cropping year. The metabolites most reduced after intercropping were negatively correlated with the beneficial taxa Bacillus, Pseudomonas, Nitrobacter, and Penicillium. Thus, intercropping drove changes in root exudate metabolites, which subsequently shaped the rhizosphere microbiome by increasing microbial diversity. This consequently improved soil nutrients and reduced disease in the consecutive monocultures.

Replant disease caused by negative plant-soil feedback commonly occurs in a Pseudostellaria heterophylla monoculture regime. Here, barcoded pyrosequencing of 16S ribosomal DNA amplicons combined with phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis was applied to study the shifts in soil bacterial community structure and functional potentials in the rhizosphere of P. heterophylla under consecutive monoculture and different soil amendments (i.e., bio-organic fertilizer application [MF] and paddy-upland rotation [PR]). The results showed that the yield of tuberous roots decreased under P. heterophylla consecutive monoculture and then increased after MF and PR treatments, which was consistent with the changes in soil bacterial diversity. Both principal coordinate analysis and the unweighted pair-group method with arithmetic means cluster analysis showed the distinct difference in bacterial community structure between the consecutively monocultured soil (relatively unhealthy soil) and other relatively healthy soils (i.e., newly planted soil, MF, and PR). Furthermore, taxonomic analysis showed that consecutive monoculture of P. heterophylla significantly decreased the relative abundances of the families Burkholderiaceae and Acidobacteriaceae (subgroup 1), whereas it increased the population density of families Xanthomonadaceae, Phyllobacteriaceae, Sphingobacteriaceae, and Alcaligenaceae, and Fusarium oxysporum. In contrast, the MF and PR treatments recovered the soil microbiome and decreased F. oxysporum abundance through the different ways; for example, the introduction of beneficial microorganisms (in MF) or the switching between anaerobic and aerobic conditions (in PR). In addition, PICRUSt analysis revealed the higher abundances of membrane transport, cell motility, and DNA repair in the consecutively monocultured soil, which might contribute to the root colonization and survival for certain bacterial pathogens under monoculture. These findings highlight the close association between replant disease of P. heterophylla and the variations in structure and potential functions of rhizosphere bacterial community.

The root exudates of Radix pseudostellariae, working as a rhizospheric intermediary between plants and microbes, can deteriorate the microbial community in the rhizosphere in a consecutive monoculture system. We assessed the effects of artificially applied R. pseudostellariae root exudates on R. pseudostellariae seedling growth, rhizosphere soil microbial communities, and soil physicochemical properties. We found that phenolic acids and organic acids acted as a driver of changes in the microbial community. High-throughput sequencing and qRT-PCR analysis demonstrated that treatment with phenolic acids significantly decreased the relative abundance of Trichoderma, Penicillium, Pseudomonadales, Xanthomonadales, and Streptomycetales. Organic acids had a significant negative effect on the relative abundance of Pseudomonadales and Streptomycetales and significantly increased the abundance of Fusarium, Xanthomonadales, Micrococcales, and Gemmatimonadales. Analysis based on the noninvasive microtest technique indicated that root exudates increased H+ efflux and plasma membrane H+-ATPase activity in the pathogenic fungi and decreased them in the beneficial fungi. These phenomena created an acidic environment for the inhibition of beneficial bacteria and accumulation of specialized plant pathogens. This study explains the mechanisms underlying the shift in microflora and structural disorder caused by root exudates in continuously monocultured R. pseudostellariae rhizosphere soil through responses to environmental conditions.

A growing problem in intensive agricultural systems is replanting disease. Application of bio-fertilizer containing beneficial microbes contributes to disease suppression and is a promising strategy to control replanting disease. However, the effect of both replanting disease and bio-fertilizer amendment on the assembly of crop microbiota in leaves and roots and their relationships to crop yield and quality remains elusive. In these experiments, roots and leaves of Radix pseudostellariae were collected from different consecutive monoculture and bio-fertilizer amended fields and characterized the associated microbiota by bacterial 16S rRNA gene sequencing and qRT-PCR. Consecutive monoculture altered the bacterial community structure and composition and significantly increased the abundance of pathogenic Ralstonia and Fusarium oxysporum in leaves and roots. Furthermore, bio-fertilizer application alleviated replanting disease by decreasing the pathogen load, increasing the beneficial genera Pseudomonas, Streptomyces, Paenibacillus, and Bradyrhizobium, and enhancing positive connections of the bacterial community across the two compartments. Bio-fertilizer had a positive and indirect effect as indicated by a structural equation models on both yield and quality by shaping the leaf microbiota rather than the root microbiota. Our findings highlight the role of leaf and root microbiota on replanting disease, showing that bio-fertilizer contributes to alleviating replanting disease by improving the plant-microbe interactions.

Under consecutive monoculture, the abundance of pathogenic fungi, such as Fusarium oxysporum in the rhizosphere of Radix pseudostellariae, negatively affects the yield and quality of the plant. Therefore, it is pertinent to explore the role of antagonistic fungi for the management of fungal pathogens such as F. oxysporum. Our PCR-denatured gradient gel electrophoresis (DGGE) results revealed that the diversity of Trichoderma spp. was significantly declined due to extended monoculture. Similarly, quantitative PCR analysis showed a decline in Trichoderma spp., whereas a significant increase was observed in F. oxysporum. Furthermore, seven Trichoderma isolates from the R. pseudostellariae rhizosphere were identified and evaluated in vitro for their potentiality to antagonize F. oxysporum. The highest and lowest percentage of inhibition (PI) observed among these isolates were 47.91 and 16.67%, respectively. In in vivo assays, the R. pseudostellariae treated with four Trichoderma isolates, having PI > 30%, was used to evaluate the biocontrol efficiency against F. oxysporum in which T. harzianum ZC51 enhanced the growth of the plant without displaying any disease symptoms. Furthermore, the expression of eight defense-related genes of R. pseudostellariae in response to a combination of F. oxysporum and T. harzianum ZC51 treatment was checked, and most of these defense genes were found to be upregulated. In conclusion, this study reveals that the extended monoculture of R. pseudostellariae could alter the Trichoderma communities in the plant rhizosphere leading to relatively low level of antagonistic microorganisms. However, T. harzianum ZC51 could inhibit the pathogenic F. oxysporum and induce the expression of R. pseudostellariae defense genes. Hence, T. harzianum ZC51 improves the plant resistance and reduces the growth inhibitory effect of consecutive monoculture problem.

A field experiment with five nitrogen (N) application rates (120, 140, 160, 180, 200 kg hm−2) under peanut/maize intercropping regime was conducted to evaluate cropping patterns and N application rates on yield, soil enzyme activities, and rhizosphere microbial community structure. The field experiment showed that the land equivalent ratio (LER) in maize/peanut intercropping system was not decreased as compared with the monoculture pattern, though the total N supply was approximately reduced by 20%. Terminal restriction fragment length polymorphism (T-RFLP) results showed that the treatments of intercropping (IMP100%, IMP80% and IMP60%) increased the abundance of Rhizobium hainanense, Rhizobium leguminosarum and Frankia which are associated with nitrogen fixation as compared to monoculture pattern (M100% and P100%). The qPCR results revealed that the copy number of nifH was significantly higher in the treatments of intercropping than in monoculture pattern. The result was also consistent with the T-RFLP analysis. In conclusion, peanut and maize under the condition of intercropping can promote the population of microorganisms associated with nitrogen-fixing in the rhizospheric soil. Our results provide a theoretical basis and technical support to soil N utilization, development of low carbon agriculture and protection of farmland ecological environment.

Replant disease caused by negative plant-soil feedback commonly occurs in a

Nitrogen (N) is one of the indispensable factors in rice growth and development. China holds a premier position in the production of rice and at the same time also faces higher N fertilizer costs along with serious damage to the environment. A better solution is much needed to address these issues, without disrupting the production of rice as an important cereal, while minimizing all the deleterious effects on the environment. Two isogenic lines Kitaake (WT) and its genetically modified line CIPK2 (RC), overexpressing the gene for Calcineurin B-like interacting protein kinase 2 (OsCIPK2) with better nitrogen use efficiency (NUE), were compared for their growth and development under low versus normal levels of N. NUE is a complex trait mainly related to a plant’s efficiency in extraction, assimilation, and recycling of N from soil. The microbial population was analyzed using high-throughput Illumina Miseq 16S rRNA sequencing and found that RC with CIPK2, specifically expressed in rice root, not only performed better without nitrogen fertilizer (LN) but also increased the diversity of bacterial communities in rice rhizosphere compartments (rhizosphere, rhizoplane, and endosphere). The relative abundance of beneficial bacteria phyla increased, which are known to promote the circulation and transformation of N in rhizosphere soil. To further explore the potential of RC regarding better performance under LN, the ion fluxes in root apical were detected by non-invasive micro-test technique (NMT). We found that RC can absorb more Ca2+ and NO3− under LN as compared to WT. Finally, compared to WT, RC plants exhibited better growth of root and shoot, and increased yield and N uptake under LN, whereas there was no significant difference in the growth of two rice lines under normal nitrogen (NN) treatment. We are able to get preliminary results, dealing with the OsCIPK2 overexpressed rice line, by studying the rice molecular, physiological, and chemical parameters related to NUE. The results laid the foundation for further research on N absorption and utilization in rice from the soil and the interaction with microbial communities.

Seasonal shifts play an important role in soil microbial community composition. This study examined thehypothesis that soil microbial community structure would vary with seasonal shifts in the Wuyi Mountainsin Southeast China, and that two representative tree species (Castanopisi carlesii and Cunninghamia lanceolata) may have different soil microbial community composition.Phospholipids fatty acid analysis (PLFA) was used toassess the effect of seasonal shifts and vegetationtypes on soil microbial community structure. A total of 22 different PLFAswere identified from all the soil samples. The bacterial PLFAs accounted for 62.37% of the total PLFAs, followed byfungi (28.94%), and the minimum was actinomycetes (6.41%). Overall, the level of PLFAs in C. carlesii soil wasgreater than those in C. lanceolata soil, and significant differences were observed in some seasons. The amounts of total,bacteria, actinomycic and fungal PLFAs significantly changed with the seasons and followed a sequence order(summer > autumn > spring > winter). The bacteria/fungi PLFAs and G (+) /G (-) PLFAs of two vegetationtypes alsochanged with the seasons and the ratios in summer and autumn were higher than those in spring and winter. The correlationanalysis of microbial PLFAs and soil physicochemical properties showed that the total, bacteria, fungal, actinomycic, G(+) and G (-) PLFAs were significantly positive correlation with TOC, TN, TP, TK and moisture content. We concludedthat the seasonal shifts and vegetationtypes affect soil microbial community composition by changing the soil physicochemical properties.

Consecutive monoculture of Rehmannia glutinosa, highly valued in traditional Chinese medicine, leads to a severe decline in both quality and yield. Rhizosphere microbiome was reported to be closely associated with the soil health and plant performance. In this study, comparative metagenomics was applied to investigate the shifts in rhizosphere microbial structures and functional potentials under consecutive monoculture. The results showed R. glutinosa monoculture significantly decreased the relative abundances of Pseudomonadaceae and Burkholderiaceae, but significantly increased the relative abundances of Sphingomonadaceae and Streptomycetaceae. Moreover, the abundances of genera Pseudomonas, Azotobacter, Burkholderia, and Lysobacter, among others, were significantly lower in two-year monocultured soil than in one-year cultured soil. For potentially harmful/indicator microorganisms, the percentages of reads categorized to defense mechanisms (i.e., ATP-binding cassette (ABC) transporters, efflux transporter, antibiotic resistance) and biological metabolism (i.e., lipid transport and metabolism, secondary metabolites biosynthesis, transport and catabolism, nucleotide transport and metabolism, transcription) were significantly higher in two-year monocultured soil than in one-year cultured soil, but the opposite was true for potentially beneficial microorganisms, which might disrupt the equilibrium between beneficial and harmful microbes. Collectively, our results provide important insights into the shifts in genomic diversity and functional potentials of rhizosphere microbiome in response to R. glutinosa consecutive monoculture.

Consecutive monoculture of Rehmannia glutinosa in the same field leads to a severe decline in both quality and yield of tuberous roots, the most useful part in traditional Chinese medicine. Fungi are an important and diverse group of microorganisms in the soil ecosystem and play crucial roles in soil health. In this study, high-throughput pyrosequencing of internal transcribed spacer 2 ribosomal DNA amplicons was applied to gain insight into how consecutive monoculture practice influence and stimulate R. glutinosa rhizosphere and bulk soil fungal communities. The results from nonmetric multidimensional scaling ordination and clustering analysis revealed distinctive differences between rhizosphere and bulk soil fungal communities. However, longer-term monocultured bulk soils were more similar to the rhizosphere soils in comparison with the shorter-term monocultured bulk soils. Moreover, consecutive monoculture caused a gradual shift in the composition and structure of the soil fungal community. The cultivation of this plant led to the appearance of some exclusive operational taxonomic units in rhizosphere or bulk soils that were assigned to the genera Fusarium, Rhizoctonia, and so on. Furthermore, the sum of the relative abundance of species of Fusarium, Cylindrocarpon, and Gibberella (belonging to the family Nectriaceae); Rhizoctonia, Thanatephorus, and Ceratobasidium (belonging to the family Ceratobasidiaceae); and Lectera and Plectosporium (belonging to the family Plectosphaerellaceae) was significantly higher in consecutively monocultured (CM) than in newly planted (NP) soil in both rhizosphere and bulk soils. In particular, Fusarium abundance was significantly higher in CM than in NP in the rhizosphere, and higher in rhizosphere soils than in bulk soils for each treatment. A pathogenicity test showed that both Fusarium strains isolated were pathogenic to R. glutinosa seedlings. In addition, the culture filtrate and mycotoxins produced by Fusarium oxysporum significantly repressed the growth of the antagonistic bacterium, Pseudomonas aeruginosa. In conclusion, consecutive monoculture of R. glutinosa restructured the fungal communities in both rhizosphere and bulk soils but bulk effects developed more slowly over time in comparison with rhizosphere effects. Furthermore, microbial interactions might lead to a reduction in the abundance of beneficial microbes.

The production and quality of Rehmannia glutinosa can be dramatically reduced by replant disease under consecutive monoculture. The root-associated microbiome, also known as the second genome of the plant, was investigated to understand its impact on plant health. Culture-dependent and culture-independent pyrosequencing analysis was applied to assess the shifts in soil bacterial communities in the rhizosphere and rhizoplane under consecutive monoculture. The results show that the root-associated microbiome (including rhizosphere and rhizoplane microbiomes) was significantly impacted by rhizocompartments and consecutive monoculture. Consecutive monoculture of R. glutinosa led to a significant decline in the relative abundance of the phyla Firmicutes and Actinobacteria in the rhizosphere and rhizoplane. Furthermore, the families Flavobacteriaceae, Sphingomonadaceae, and Xanthomonadaceae enriched while Pseudomonadaceae, Bacillaceae, and Micrococcaceae decreased under consecutive monoculture. At the genus level, Pseudomonas, Bacillus, and Arthrobacter were prevalent in the newly planted soil, which decreased in consecutive monocultured soils. Besides, culture-dependent analysis confirmed the widespread presence of Pseudomonas spp. and Bacillus spp. in newly planted soil and their strong antagonistic activities against fungal pathogens. In conclusion, R. glutinosa monoculture resulted in distinct root-associated microbiome variation with a reduction in the abundance of beneficial microbes, which might contribute to the declined soil suppressiveness to fungal pathogens in the monoculture regime.

Intercropping has been widely used to control disease and improve yield in agriculture. In this study, maize and peanut were used for non-separation intercropping (NS), semi-separation intercropping (SS) using a nylon net, and complete separation intercropping (CS) using a plastic sheet. In field experiments, two-year land equivalent ratios (LERs) showed yield advantages due to belowground interactions when using NS and SS patterns as compared to monoculture. In contrast, intercropping without belowground interactions (CS) showed a yield disadvantage. Meanwhile, in pot experiments, belowground interactions (found in NS and SS) improved levels of soil-available nutrients (nitrogen (N) and phosphorus (P)) and enzymes (urease and acid phosphomonoesterase) as compared to intercropping without belowground interactions (CS). Soil bacterial community assay showed that soil bacterial communities in the NS and SS crops clustered together and were considerably different from the CS crops. The diversity of bacterial communities was significantly improved in soils with NS and SS. The abundance of beneficial bacteria, which have the functions of P-solubilization, pathogen suppression, and N-cycling, was improved in maize and peanut soils due to belowground interactions through intercropping. Among these bacteria, numbers of Bacillus, Brevibacillus brevis, and Paenibacillus were mainly increased in the maize rhizosphere. Burkholderia, Pseudomonas, and Rhizobium were mainly increased in the peanut rhizosphere. In conclusion, using maize and peanut intercropping, belowground interactions increased the numbers of beneficial bacteria in the soil and improved the diversity of the bacterial community, which was conducive to improving soil nutrient (N and P) supply capacity and soil microecosystem stability.

Consecutive monoculture leads to a substantial decline in both yield and quality for Rehmannia glutinosa. The diversity of microbes in rhizosphere can affect plant health. The objective was to investigate the effects of consecutive monoculture of this plant on rhizospheric microbial community composition and catabolic diversity at different stages of plant growth. The results showed that the microbial communities were significantly affected by both longevity of monoculture and plant growth stage. The amounts of phospholipid fatty acids indicative of most microbial functional groups differed significantly between the newly planted and monocultured soils. In addition, a significant correlation was observed between the microbial biomass and the community metabolic activities. The cyclopropyl-to-precursor ratio (cy/pre), an indicator of physiological stress in microbial communities, was significantly higher in the monocultured soils than in the newly planted soil at both the root elongation and expansion stages. Furthermore, the amounts of two pathogenic fungi (Fusarium oxysporum and Aspergillus flavus) significantly increased with increasing years of monoculture. In conclusion, we revealed characteristic differences in the microbial community composition and functions in R. glutinosa rhizosphere after monoculture, which might be attributed to the changes in plant performance and root exudates.

Background Pseudostellaria heterophylla (P. heterophylla), a herbaceous perennial, belongs to Caryophyllaceae family and is one of the Chinese herbal medicine with high pharmacodynamic value. It can be used to treat the spleen deficiency, anorexia, weakness after illness and spontaneous perspiration symptoms. Our previous study found that consecutive monoculture of Pseudostellaria heterophylla could lead to the deterioration of the rhizosphere microenvironment. The specialized forms of pathogenic fungus Fusarium oxysporum f.Sp. heterophylla (F. oxysporum) in rhizosphere soils of P. heterophylla plays an important role in the consecutive monoculture of P. heterophylla. Results In this study, F. oxysporum was used to infect the tissue culture plantlets of P. heterophylla to study the responding process at three different infection stages by using RNA-sequencing. We obtained 127,725 transcripts and 47,655 distinct unigenes by de novo assembly and obtained annotated information in details for 25,882 unigenes. The Kyoto Encyclopedia of Genes and Genomes pathway analysis and the real-time quantitative PCR results suggest that the calcium signal system and WRKY transcription factor in the plant-pathogen interaction pathway may play an important role in the response process, and all of the WRKY transcription factor genes were divided into three different types. Moreover, we also found that the stimulation of F. oxysporum may result in the accumulation of some phenolics in the plantlets and the programmed cell death of the plantlets. Conclusions This study has partly revealed the possible molecular mechanism of the population explosion of F. oxysporum in rhizosphere soils and signal response process, which can be helpful in unraveling the role of F. oxysporum in consecutive monoculture problems of P. heterophylla. Electronic supplementary material The online version of this article (10.1186/s12870-017-1106-3) contains supplementary material, which is available to authorized users.

A three-year field monoculture trial of Radix pseudostellariae and complementary laboratory studies were conducted to further elucidate the underlying mechanism responsible for significant decreases in the biomass yield and quality of R. pseudostellariae under continuous monoculture regimes. HPLC analysis indicated that continuous monoculture soil was rich in organic acids, which had cumulative effects over time. Further analysis suggested that the application of a mixture of organic acids significantly promoted growth of pathogenic fungi, and increased the expression of chemotaxis-related gene (cheA) and biofilm formation of the specific pathogenic Kosakonia sacchari. However, opposite reactions were observed in the case of Bacillus megaterium and Bacillus pumilus. Concurrently, the present results revealed that the mixed organic acids stimulated the production of toxins, as well as H2O2 in the pathogenic fungi. Furthermore, the presence of organic acids reflecting environmental conditions under monocropping had negative effects on the expression of the biocontrol-related genes, which resulted in attenuated antagonistic activities of plant growth-promoting rhizobacteria (PGPR) to suppress mycelial growth of the pathogenic fungi. These results help to unveil the mechanisms associated with how accumulated organic acids differentially mediate deterioration of soil microbial composition and structure in monocropping system.

This paper presents a 20 Mfps 32 × 84 pixels CMOS burst-mode imager featuring high frame depth with a passive in-pixel amplifier. Compared to the CCD alternatives, CMOS burst-mode imagers are attractive for their low power consumption and integration of circuitry such as ADCs. Due to storage capacitor size and its noise limitations, CMOS burst-mode imagers usually suffer from a lower frame depth than CCD implementations. In order to capture fast transitions over a longer time span, an in-pixel CDS technique has been adopted to reduce the required memory cells for each frame by half. Moreover, integrated with in-pixel CDS, an in-pixel NMOS-only passive amplifier alleviates the kTC noise requirements of the memory bank allowing the usage of smaller capacitors. Specifically, a dense 108-cell MOS memory bank (10fF/cell) has been implemented inside a 30μm pitch pixel, with an area of 25 × 30μm2 occupied by the memory bank. There is an improvement of about 4x in terms of frame depth per pixel area by applying in-pixel CDS and amplification. With the amplifier’s gain of 3.3, an FD input-referred RMS noise of 1mV is achieved at 20 Mfps operation. While the amplification is done without burning DC current, including the pixel source follower biasing, the full pixel consumes 10μA at 3.3V supply voltage at full speed. The chip has been fabricated in imec’s 130nm CMOS CIS technology. © (2017) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

Nitrogen (N) is one of the indispensable factors in rice growth and development. China holds a premier position in the production of rice and at the same time also faces higher N fertilizer costs along with serious damage to the environment. A better solution is much needed to address these issues, without disrupting the production of rice as an important cereal, while minimizing all the deleterious effects on the environment. Two isogenic lines Kitaake (WT) and its genetically modified line CIPK2 (RC), overexpressing the gene for Calcineurin B-like interacting protein kinase 2 (OsCIPK2) with better nitrogen use efficiency (NUE), were compared for their growth and development under low versus normal levels of N. NUE is a complex trait mainly related to a plant&rsquo, s efficiency in extraction, assimilation, and recycling of N from soil. The microbial population was analyzed using high-throughput Illumina Miseq 16S rRNA sequencing and found that RC with CIPK2, specifically expressed in rice root, not only performed better without nitrogen fertilizer (LN) but also increased the diversity of bacterial communities in rice rhizosphere compartments (rhizosphere, rhizoplane, and endosphere). The relative abundance of beneficial bacteria phyla increased, which are known to promote the circulation and transformation of N in rhizosphere soil. To further explore the potential of RC regarding better performance under LN, the ion fluxes in root apical were detected by non-invasive micro-test technique (NMT). We found that RC can absorb more Ca2+ and NO3&minus, under LN as compared to WT. Finally, compared to WT, RC plants exhibited better growth of root and shoot, and increased yield and N uptake under LN, whereas there was no significant difference in the growth of two rice lines under normal nitrogen (NN) treatment. We are able to get preliminary results, dealing with the OsCIPK2 overexpressed rice line, by studying the rice molecular, physiological, and chemical parameters related to NUE. The results laid the foundation for further research on N absorption and utilization in rice from the soil and the interaction with microbial communities.

Rehmannia glutinosa, a widely used Chinese medicinal herb, has been shown to suffer from serious consecutive monoculture problems that cause significant decline in both yield and quality. The objective of this study was to evaluate the response of the soil microbial community and the effect on catabolic diversity to consecutive monoculture regime using three different techniques: substrate-induced respiration (SIR), phospholipid fatty acid (PLFA) and community-level physiological profiles (CLPP) analyses. We found that basal soil respiration (BSR) was significantly higher in the control and newly planted soils than in the second and third year consecutive monoculture soils. However, no significant difference was observed in SIR among the newly planted, second and third year consecutive monoculture soils. The PLFA signatures indicated that the bacterial biomass was larger than the fungal biomass in all four treatments and both enhanced with the increasing years of monoculture and attained the peak in SM. The ratio of cyclopropyl PLFAs to their metabolic precursors (cy/pre), a measure of physiological stress in microbial communities, in the second and third year consecutive monoculture soils was significantly greater than that in the control and newly planted soils. Biolog analysis results revealed that the consumption of carboxylic acids, phenolic acids and amines, especially acid carbon substrates, in the consecutively monocultured soil was significantly greater than that in the newly planted soil. Both PLFA- and CLPP-based principal component analysis (PCA) and cluster analysis revealed the distinct separation between the control, newly planted plots and the second, third year consecutive monoculture plots. Through our PLFA-based and Biolog analysis, together with microbial respiration determination, we were able to reveal characteristic differences in the microbial community composition and activities in the rhizosphere following R. glutinosa monoculture.

The Real-time quantitative PCR primers of the differential expression unigenes. (DOCX 15Â kb)

The annotated unigenes statistics analysis. (DOCX 13Â kb)

This paper reports on a Time Delay and Integration image sensor System-on-Chip realized in an embedded CCD process. The integration of single-poly CCD modules into a standard 0.13?m CMOS process is discussed. The technology performance has been evaluated using dedicated test structures. Next, a prototype TDI imager with 5?m pixel pitch, 512 rows and 1024 columns was designed, manufactured and characterized. Charge Transfer Efficiency greater than 0.9999 up till very high line rates of 400kHz was recorded.

Under consecutive monoculture, the biomass and quality of Pseudostellaria heterophylla declines significantly. In this study, a three-year field experiment was conducted to identify typical growth inhibition effects caused by extended monoculturing of P. heterophylla. Deep pyrosequencing was used to examine changes in the structure and composition of soil fungal community along a three-year gradient of monoculture. The results revealed a distinct separation between the newly planted plot and the two-year, three-year monocultured plots. The Shannon and Simpson diversity indices were significantly higher in the two-year and three-year monoculture soils than in the newly planted soil. Consecutive monoculture of this plant led to a significant increase in relative abundance of Fusarium, Trichocladium and Myrothecium and Simplicillium, etc., but a significant decrease in the relative abundance of Penicillium. Quantitative PCR analysis confirmed a significant increase in Fusarium oxysporum, an agent known to cause wilt and rot disease of P. heterophylla. Furthermore, phenolic acid mixture at a ratio similar to that found in the rhizosphere could promote mycelial growth of pathogenic F. oxysporum. Overall, this study demonstrated that consecutive monoculture of P. heterophylla can alter the fungal community in the rhizosphere, including enrichment of host-specific pathogenic fungi at the expense of plant-beneficial fungi.

Three experiments were conducted to study the allelopathic stimulation and its underlying molecular mechanism of achyranthes medicinal plants in continuously monoculture system. The stimulators in the rhizospheric soil of continuously monocultured achyranthes plants were extracted by water and organic solvents. Results of the bioassay showed that the rhizospheric soil extracts had a significant promotive effect on the growth of achyranthes in continuous monoculture system, implying that the extracts, especially the water extracts might contain plant activators to stimulate the growth of the medicinal plants. Subtractive hybridization suppression (SSH) was used to investigate gene expression profiles of achyranthes in response to the extract treatments. Ten up-regulated genes from SSH-cDNA library were sequenced and assigned. Results indicated that flavonoids and phytosterol might play an important role in the positively allelopathic stimulation on achyranthes plants in continuous monoculture system. Comparative proteomics were employed to further unveil the molecular mechanism of allelopathic stimulation induced by the extracts. Compared with protein expression profile in control, 25 differentially expressed proteins and their functions were detected and identified in the treated plants. The results suggested that the extracts from continuously monocultured rhizospheric soils under Chinese medicinal achyranthes activated the genes encoding the key enzymes involved in terpenes and flavonoids synthesis, which in turn led to increased de novo synthesis of the stimulators, and hence promoted growth of achyranthes in consecutively monoculture system.

Soil rhizospheric metaproteomics is a powerful scientific tool to uncover the interactions between plants and microorganisms in the soil ecosystem. The present study established an extraction method suitable for different soils that could increase the extracted protein content. Close to 1000 separate spots with high reproducibility could be identified in the stained 2-DE gels. Among the spots, 189 spots representing 122 proteins on a 2-DE gel of rice soil samples were successfully identified by MALDI-TOF/TOF-MS. These proteins mainly originated from rice and microorganisms. They were involved in protein, energy, nucleotide, and secondary metabolisms, as well as signal transduction and resistance. Three characteristics of the crop rhizospheric metaproteomics seemed apparent: (1) approximately one-third of the protein spots could not be identified by MALDI-TOF/TOF/MS, (2) the conservative proteins from plants formed a feature distribution of crop rhizospheric metaproteome, and (3) there were very complex interactions between plants and microorganisms existing in a crop rhizospheric soil. Further functional analysis on the identified proteins unveiled various metabolic pathways and signal transductions involved in the soil biotic community. This study provides a paradigm for metaproteomic research on soil biology.