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    农业生态环境-土壤微生物合辑Agro-ecosystem & Environment—Soil microbe

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    Silicon impacts on soil microflora under Ralstonia Solanacearum inoculation
    LIN Wei-peng, JIANG Ni-hao, PENG Li, FAN Xue-ying, GAO Yang, WANG Guo-ping, CAI Kun-zheng
    2020, 19 (1): 251-264.   DOI: 10.1016/S2095-3119(18)62122-7
    Abstract80)      PDF in ScienceDirect      
    Silicon (Si) can increase plant resistance against bacterial wilt caused by Ralstonia solanacearum and enhance plant immune response.  However, whether Si alleviates soil-borne disease stress through altering soil microbial community component and diversity is not clear.  In this study, effects of Si application under R. solanacearum inoculation with or without plant on soil bacterial and fungal communities were investigated through high-throughput pyrosequencing technique.  The results showed that Si addition significantly reduced bacterial wilt incidence.  However, Si did not reduce the amount of R. solanacearum in rhizosphere soil.  Principal components analysis showed that soil microbial community composition was strongly influenced by Si addition.  Total 63.7% bacterial operational taxonomic units (OTUs) and 43.8% fungal OTUs were regulated by Si addition regardless of the presence of tomato plants, indicating the independent effects of Si on soil microbial community.  Si-added soil harbored a lower abundance of Fusarium, Pseudomonas, and Faecalibacterium.  Our finding further demonstrated that exogenous Si could significantly influence soil microbial community component, and this may provide additional insight into the mechanism of Si-enhanced plant resistance against soil-borne pathogens.
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    A comprehensive analysis of the response of the fungal community structure to long-term continuous cropping in three typical upland crops
    LIU Hang, PAN Feng-juan, HAN Xiao-zeng, SONG Feng-bin, ZHANG Zhi-ming, YAN Jun, XU Yan-li
    2020, 19 (3): 866-880.   DOI: 10.1016/S2095-3119(19)62630-4
    Abstract54)      PDF in ScienceDirect      
    Certain agricultural management practices are known to affect the soil microbial community structure; however, knowledge of the response of the fungal community structure to the long-term continuous cropping and rotation of soybean, maize and wheat in the same agroecosystem is limited.  We assessed the fungal abundance, composition and diversity among soybean rotation, maize rotation and wheat rotation systems and among long-term continuous cropping systems of soybean, maize and wheat as the effect of crop types on fungal community structure.  We compared these fungal parameters of same crop between long-term crop rotation and continuous cropping systems as the effect of cropping systems on fungal community structure.  The fungal abundance and composition were measured by quantitative real-time PCR and Illumina MiSeq sequencing.  The results revealed that long-term continuous soybean cropping increased the soil fungal abundance compared with soybean rotation, and the fungal abundance was decreased in long-term continuous maize cropping compared with maize rotation.  The long-term continuous soybean cropping also exhibited increased soil fungal diversity.  The variation in the fungal community structure among the three crops was greater than that between long-term continuous cropping and rotation cropping.  Mortierella, Guehomyces and Alternaria were the most important contributors to the dissimilarity of the fungal communities between the continuous cropping and rotation cropping of soybean, maize and wheat.  There were 11 potential pathogen and 11 potential biocontrol fungi identified, and the relative abundance of most of the potential pathogenic fungi increased during the long-term continuous cropping of all three crops.  The relative abundance of most biocontrol fungi increased in long-term continuous soybean cropping but decreased in long-term continuous maize and wheat cropping.  Our results indicate that the response of the soil fungal community structure to long-term continuous cropping varies based upon crop types.
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    Screening and degradation characteristics of a tylosin-degrading strain
    FENG Chang-qing, CHENG Deng-miao, FENG Yao, QI Wei-ning, JIA Zhen-hu, Louise WEAVER, LIU Yuan-wang, LI Zhao-jun
    2020, 19 (4): 1127-1136.   DOI: 10.1016/S2095-3119(19)62764-4
    Abstract68)      PDF in ScienceDirect      
    Antibiotics residues have been accumulating in the environment day by day due to overuse of antibiotics.  Recalcitrant antibiotic residues, such as tylosin (TYL), can cause serious environmental problems, which makes it important to eliminate TYL from the environment.  It is important to eliminate TYL from the environment.  In this study, a strain was isolated and purified from fermentation by-product that came from a TYL production factory.  The TYL degrading strain was identified by its morphology, physiological and biochemical reactions and sequencing the PCR-amplified fragments of its 16S rDNA-coding genes.  The temperature, shaking speed, initial TYL concentration, pH and inoculum sizes were investigated under simulated conditions by using single factor tests.  The results showed that TYL2, a high efficient strain was isolated and was identified as Brevibacillus borstelensis.  The degradation rate of TYL by this strain could reach to 75% with an initial concentration of 25 mg L–1 within 7 days under conditions of 7% B. borstelensis (v/v, 2×108 CFU mL–1) at pH 7.0 and at 35°C.  It is interesting that this strain has a very strong ability to degrade the TYL in natural sewage with the degradation rate of 65% within 7 days.  This result could be helpful for the degradation of TYL and provide guidance for the degradation of other antibiotics.
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    Long-term fertilization leads to specific PLFA finger-prints in Chinese Hapludults soil
    WANG Qi-qi, LIU Ling-ling, LI Yu, QIN Song, WANG Chuan-jie, CAI An-dong, WU Lei, XU Ming-gang, ZHANG Wen-ju
    2020, 19 (5): 1354-1362.   DOI: 10.1016/S2095-3119(19)62866-2
    Abstract68)      PDF in ScienceDirect      
    Soil microbes play essential roles in the biogeochemical processes of organic carbon and nutrient cycling.  Many studies have reported various short-term effects of fertilization on soil microbes.  However, less is known about the effects of long-term fertilization regimes on the rhizosphere.  Therefore, the objective of this study was to explore how the soil microbial communities in the rhizosphere respond to different long-term fertilization strategies.  Based on a 21-year field treatment experiment in Guizhou, China, we extracted phospholipid fatty acids (PLFAs) to determine the microbial community structure in both the non-rhizosphere (NR) and rhizosphere (R).  Six treatments were included: no fertilizer (CK), mineral nitrogen fertilizer (N), N with potassium (NK), phosphorus with K (PK), NPK, and NPK combined with manure (MNPK).  The results showed that total PLFAs under unbalanced mineral fertilization (N, NK and PK) were decreased by 45% on average in the NR compared with CK, whereas MNPK increased fungi and G–bacteria abundance significantly in both the NR (by 33 and 23%) and R (by 15 and 20%), respectively.  In addition, all microbial groups in the R under these treatments (N, NK and PK) were significantly increased relative to those in the NR, except for the ratio of F/B and G+/G–, which might be due to the high nutrient availability in the R.  Soil pH and SOC significantly regulated the soil microbial community and structure, explaining 51 and 20% of the variation in the NR, respectively.  However, the rhizosphere microbial community structure was only significantly affected by soil pH (31%).  We concluded that the soil microbial community in the NR was more strongly affected by long-term fertilization than that in the R due to the rhizosphere effect in the agricultural ecosystem.  Rhizosphere nutrient conditions and buffering capacity could help microbial communities resist the change from the long-term fertilization.
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    Aggregate-associated changes in nutrient properties, microbial community and functions in a greenhouse vegetable field based on an eight-year fertilization experiment of China
    LUAN Hao-an, GAO Wei, TANG Ji-wei, LI Ruo-nan, LI Ming-yue, ZHANG Huai-zhi, CHEN Xin-ping, Dainius MASILIUNAS, HUANG Shao-wen
    2020, 19 (10): 2530-2548.   DOI: 10.1016/S2095-3119(20)63269-5
    Abstract86)      PDF in ScienceDirect      
    Soil aggregation, microbial community, and functions (i.e., extracellular enzyme activities; EEAs) are critical factors affecting soil C dynamics and nutrient cycling.  We assessed soil aggregate distribution, stability, nutrients, and microbial characteristics within >2, 0.25–2, 0.053–0.25, and <0.053 mm aggregates, based on an eight-year field experiment in a greenhouse vegetable field in China.  The field experiment includes four treatments: 100% N fertilizer (CF), 50% substitution of N fertilizer with manure (M), straw (S), and manure plus straw (MS).  The amounts of nutrient (N, P2O5, and K2O) input were equal in each treatment.  Results showed higher values of mean weight diameter in organic-amended soils (M, MS, and S, 2.43–2.97) vs. CF-amended soils (1.99).  Relative to CF treatment, organic amendments had positive effects on nutrient (i.e., available N, P, and soil organic C (SOC)) conditions, microbial (e.g., bacterial and fungal) growth, and EEAs in the >0.053 mm aggregates, but not in the <0.053 mm aggregates.  The 0.25–0.053 mm aggregates exhibited better nutrient conditions and hydrolytic activity, while the <0.053 mm aggregates had poor nutrient conditions and higher oxidative activity among aggregates, per SOC, available N, available P, and a series of enzyme activities.  These results indicated that the 0.25–0.053 mm (<0.053 mm) aggregates provide suitable microhabitats for hydrolytic (oxidative) activity.  Interestingly, we found that hydrolytic and oxidative activities were mainly impacted by fertilization (58.5%, P<0.01) and aggregate fractions (50.5%, P<0.01), respectively.  The hydrolytic and oxidative activities were significantly (P<0.01) associated with nutrients (SOC and available N) and pH, electrical conductivity, respectively.  Furthermore, SOC, available N, and available P closely (P<0.05) affected microbial communities within >0.25, 0.25–0.053, and <0.053 mm aggregates, respectively.  These findings provide several insights into microbial characteristics within aggregates under different fertilization modes in the greenhouse vegetable production system in China.
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    Pseudomonas sp. TK35-L enhances tobacco root development and growth by inducing HRGPnt3 expression in plant lateral root formation
    CAO Yuan-yuan, NI Hai-ting, LI Ting, LAY Khien-duc, LIU Dai-song, HE Xiang-yi, OU Kang-miao, TANG Xin-yun, WANG Xiao-bo, Qiu Li-juan
    2020, 19 (10): 2549-2560.   DOI: 10.1016/S2095-3119(20)63266-X
    Abstract75)      PDF in ScienceDirect      
    Rhizosphere colonization is a key requirement for the application of plant growth-promoting rhizobacteria (PGPR) as a biofertilizer.  Signaling molecules are often exchanged between PGPR and plants, and genes in plants may respond to the action of PGPR.  Here, the luciferase luxAB gene was electrotransformed into Pseudomonas sp. strain TK35, a PGPR with an affinity for tobacco, and the labelled TK35 (TK35-L) was used to monitor colonization dynamics in the tobacco rhizosphere and evaluate the effects of colonization on tobacco growth and root development.  The transcript levels of the hydroxyproline-rich glycoprotein HRGPnt3 gene, a lateral root induction indicator, in tobacco roots were examined by qPCR.  The results showed that TK35-L could survive for long periods in the tobacco rhizosphere and colonize new spaces in the tobacco rhizosphere following tobacco root extension, exhibiting significant increases in root development, seedling growth and potassium accumulation in tobacco plants.  The upregulation of HRGPnt3 transcription in the inoculated tobacco suggested that TK35-L can promote tobacco root development by upregulating the transcript levels of the HRGPnt3 gene, which promotes tobacco seedling growth.  These findings lay a foundation for future studies on the molecular mechanism underlying the plant growth-promoting activities of PGPR.  Furthermore, this work provided an ideal potential strain for biofertilizer production.
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    Contrasting resilience of soil microbial biomass, microbial diversity and ammonification enzymes under three applied soil fumigants
    SUN Zhen-cai, LI Gui-tong, ZHANG Cheng-lei, WANG Zhi-min, LIN Qi-mei, ZHAO Xiao-rong
    2020, 19 (10): 2561-2570.   DOI: 10.1016/S2095-3119(20)63201-4
    Abstract65)      PDF in ScienceDirect      
    Fumigation is a widely applied approach to mitigate the soil-borne diseases.  However, the potential effects of currently applied fumigants on ammonification remain unclear.  An 84-day incubation experiment was conducted based on non-fumigated soil (CK) and fumigated soil using three common fumigants, i.e., chloropicrin (CP), 1,3-dichloropropene (1,3-D), and metam sodium (MS).  The results showed that, the three fumigants all decreased the microbial C, and the largest reduction (84.7%) occurred with the application of CP.  After fumigation, the microbial diversity in the CP treatment rapidly recovered, but that in the 1,3-D treatment decreased and did not recover by the end of the experiment.  The application of MS showed no impact on the microbial diversity during the assay, indicating that significantly different microbial diversity can be achieved by choosing different fumigants.  Furthermore, the three fumigants showed divergent effects on the enzymes involved in ammonification.  The analysis showed that the enzyme variation with CP application was mainly associated with the changed microbial C and N (P<0.05), and not with the microbial community, which was different from the observed effects of 1,3-D or MS application.  In addition, the soil quality index showed that CP was still significantly harmful at the end of incubation compared with the good resilience of MS, indicating that CP may not be a suitable fumigant.
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    Effects of long-term straw return on soil organic carbon fractions and enzyme activities in a double-cropped rice paddy in South China
    HUANG Wan, WU Jian-fu, PAN Xiao-hua, TAN Xue-ming, ZENG Yong-jun, SHI Qing-hua, LIU Tao-ju, ZENG Yan-hua
    2021, 20 (1): 236-247.   DOI: 10.1016/S2095-3119(20)63347-0
    Abstract146)      PDF in ScienceDirect      
    Long-term straw return is an important carbon source for improving soil organic carbon (SOC) stocks in croplands, and straw removal through burning is also a common practice in open fields in South China.  However, the specific effects of long-term rice straw management on SOC fractions, the related enzyme activities and their relationships, and whether these effects differ between crop growing seasons remain unknown.  Three treatments with equal nitrogen, phosphorus, and potassium nutrient inputs, including straw/ash and chemical nutrients, were established to compare the effects of straw removal (CK), straw return (SR), and straw burned return (SBR).  Compared to CK, long-term SR tended to improve the yield of early season rice (P=0.057), and significantly increased total organic carbon (TOC) and microbial biomass carbon (MBC) in double-cropped rice paddies.  While SBR had no effect on TOC, it decreased light fraction organic carbon (LFOC) in early rice and easily oxidizable organic carbon (EOC) in late rice, significantly increased dissolved organic carbon (DOC), and significantly decreased soil pH.  These results showed that MBC was the most sensitive indicator for assessing changes of SOC in the double-cropped rice system due to long-term straw return.  In addition, the different effects on SOC fraction sizes between SR and SBR were attributed to the divergent trends in most of the soil enzyme activities in the early and late rice that mainly altered DOC, while DOC was positively affected by β-xylosidase in both early and late rice.  We concluded that straw return was superior to straw burned return for improving SOC fractions, but the negative effects on soil enzyme activities in late rice require further research.
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    The ciliate protozoan Colpoda cucullus can improve maize growth by transporting soil phosphates
    ZHANG Wen-li, LIN Qi-mei, Li Gui-tong, ZHAO Xiao-rong
    2022, 21 (3): 855-861.   DOI: 10.1016/S2095-3119(21)63628-6
    Abstract65)      PDF in ScienceDirect      
    Little is known regarding the ability of protozoans to transfer phosphates and improve maize growth.  The objective of this study was to determine whether Colpoda cucullus could improve the maize phosphorus (P) level by transferring phosphate.  In this three-compartment root box study, the soil in the outer compartment was inoculated with the common ciliate, C. cucullus, together with the addition of either KH232PO4, rock phosphate (RP), super phosphate (SP) or ammonium phosphate (AP), and then maize was grown in the inner compartment.  The results showed that the maize plants grown in the soil inoculated with C. cucullus had much higher 32P radioactivity than the control.  Colpoda cucullus inoculation resulted in significant increases in dry matter by up to 25.07%, and nitrogen (N), P and potassium (K) absorption by 1–36% (P<0.05).  Soil available P in the inner compartment of the root box was also enhanced by at least 30% due to the ciliate inoculation (P<0.05).  It was therefore suggested that phosphates might be transported from the outer to inner compartments by the inoculated C. cucullus and then absorbed by the maize plant. 
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    Microbial community dynamics during composting of animal manures contaminated with arsenic, copper, and oxytetracycline
    Ebrahim SHEHATA, CHENG Deng-miao, MA Qian-qian, LI Yan-li, LIU Yuan-wang, FENG Yao, JI Zhen-yu, LI Zhao-jun
    2021, 20 (6): 1649-1659.   DOI: 10.1016/S2095-3119(20)63290-7
    Abstract81)      PDF in ScienceDirect      
    Effects of the heavy metal copper (Cu), the metalloid arsenic (As), and the antibiotic oxytetracycline (OTC) on bacterial community structure and diversity during cow and pig manure composting were investigated.  Eight treatments were applied, four to each manure type, namely cow manure with: (1) no additives (control), (2) addition of heavy metal and metalloid, (3) addition of OTC and (4) addition of OTC with heavy metal and metalloid; and pig manure with: (5) no additives (control), (6) addition of heavy metal and metalloid, (7) addition of OTC and (8) addition of OTC with heavy metal and metalloid.  After 35 days of composting, according to the alpha diversity indices, the combination treatment (OTC with heavy metal and metalloid) in pig manure was less harmful to microbial diversity than the control or heavy metal and metalloid treatments.  In cow manure, the treatment with heavy metal and metalloid was the most harmful to the microbial community, followed by the combination and OTC treatments.  The OTC and combination treatments had negative effects on the relative abundance of microbes in cow manure composts.  The dominant phyla in both manure composts included Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria.  The microbial diversity relative abundance transformation was dependent on the composting time.  Redundancy analysis (RDA) revealed that environmental parameters had the most influence on the bacterial communities.  In conclusion, the composting process is the most sustainable technology for reducing heavy metal and metalloid impacts and antibiotic contamination in cow and pig manure.  The physicochemical property variations in the manures had a significant effect on the microbial community during the composting process.  This study provides an improved understanding of bacterial community composition and its changes during the composting process. 
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    Changes in bacterial community and abundance of functional genes in paddy soil with cry1Ab transgenic rice
    SONG Ya-na, CHEN Zai-jie, WU Ming-ji, LI Gang, WANG Feng
    2021, 20 (6): 1674-1686.   DOI: 10.1016/S2095-3119(20)63271-3
    Abstract50)      PDF in ScienceDirect      
    A field experiment involving cry1Ab transgenic rice (GM) and its parental non-cry1Ab rice (M) has been on-going since 2014.  The diversity of the bacterial communities and the abundance of the microbial functional genes which drive the conversion of nitrogen in paddy soil were analyzed during the growth period of rice in the fifth year of the experiment, using 16S rRNA-based Illumina MiSeq and real-time PCR on the amoA, nirS and nirK genes.  The results showed no differences in the alpha diversity indexes of the bacterial communities, including Chao1, Shannon and Simpson, between the fields cultivated with line GM and cultivar M at any of the growth stages of rice.  However, the bacterial communities in the paddy soil with line GM were separated from those of paddy soil with cultivar M at each of the growth stages of rice, based on the unweighted UniFrac NMDS or PCoA.  In addition, the analyses of ADONIS and ANOSIM, based on the unweighted UniFrac distance, indicated that the above separations between line GM and cultivar M were statistically significant (P<0.05) during the growth season of rice.  The increases in the relative abundances of Acidobacteria or Bacteroidetes, in the paddy soils with line GM or cultivar M, respectively, led to the differences in the bacterial communities between them.  At the same time, functional gene prediction based on Illumina MiSeq data suggested that the abundance of many functional genes increased in the paddy soil with line GM at the maturity stage of rice, such as genes related to the metabolism of starch, amino acids and nitrogen.  Otherwise, the copies of bacterial amoA gene, archaeal amoA gene and denitrifying bacterial nirK gene significantly increased (P<0.05 or 0.01) in the paddy soil with line GM.  In summary, the release of cry1Ab transgenic rice had effects on either the composition of bacterial communities or the abundance of microbial functional genes in the paddy soil.
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    Interaction of soil microbial communities and phosphorus fractions under long-term fertilization in paddy soil 
    Muhammad QASWAR, Waqas AHMED, HUANG Jing, LIU Kai-lou, ZHANG Lu, HAN Tian-fu, DU Jiang-xue, Sehrish ALI, Hafeez UR-RAHIM, HUANG Qing-hai, ZHANG Hui-min
    2022, 21 (7): 2134-2144.   DOI: 10.1016/S2095-3119(21)63733-4
    Abstract73)      PDF in ScienceDirect      
    Understanding the impact of biological activities on the soil phosphorus (P) distribution under long-term fertilizer application can facilitate better soil P fertility management.  Therefore, the primary objectives of this study were to investigate the effect of long-term (since 1981) fertilizer application on the soil P fractions and microbial community and to evaluate correlations between the microbial community structure and P distribution.  The following treatments were implemented in a long-term field trial: no fertilization (CK), inorganic N and K (NK), inorganic P and K (PK), inorganic N, P and K (NPK) and manure+NPK (MNPK) fertilization.  The study showed that the soil pH, soil organic carbon and total and available N and P concentrations were considerably higher in the MNPK treatment than in the CK treatment.  The soil microbial biomass C, N and P concentrations were also significantly higher in the MNPK treatment than in the CK treatment.  Among fertilization treatments, the β-1,4-glucosidase, α-1,4-glucosidase, urease, acid phosphatase and phosphodiesterase activities were the highest in the MNPK treatment.  Compared to inorganic fertilization, the MNPK treatment increased the labile soil P fractions and decreased the residual soil P concentration.  Continuous fertilization significantly affected the soil microbial composition.  The total phospholipid fatty acid (PLFA) concentrations in the NK, PK, NPK and MNPK treatments were 23.3, 43.1, 48.7 and 87.7% higher, respectively, than in the CK treatment.  A significant correlation was observed between the microbial community and soil P fractions.  Moreover, the aggregated boosted tree (ABT) model showed that among the various soil biochemical properties, the total PLFA concentration was the factor that most influenced the active P pool, accounting for 35.4% of the relative influence of all soil biochemical properties examined.  These findings reveal that combined manure and inorganic fertilizer application is a better approach than applying inorganic fertilizer alone for sustaining long-term P fertility by mediating soil biological activity.

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    Functional diversity of soil microbial communities in response to supplementing 50% of the mineral N fertilizer with organic fertilizer in an oat field
    ZHANG Mei-jun, JIA Ju-qing, LU Hua, FENG Mei-chen, YANG Wu-de
    2021, 20 (8): 2255-2264.   DOI: 10.1016/S2095-3119(20)63331-7
    Abstract68)      PDF in ScienceDirect      
    The effects of supplementing 50% of the mineral N fertilizer with organic fertilizer on the metabolism and diversity of soil microbial communities in an oat field were investigated using Biolog-Eco plates.  The experiment consisted of five treatments: no fertilizer (CK), mineral N fertilizer applied at 90 and 45 kg ha–1 N in the form of urea (U1 and U2, respectively), and U2 supplemented with organic fertilizer  in the form of sheep manure at 90 and 45 kg ha–1 N (U2OM1 and U2OM2, respectively).  Each treatment had three replications.  The experiment was conducted in 2018 and 2019 in Pinglu District, Shanxi Province, China.  The carbon source utilization by soil microbial communities, such as amino acids, amines, carbohydrates, carboxylic acids, and polymers, increased when 50% of the mineral N fertilizer was replaced with organic fertilizer in both years.  This result was accompanied by increased richness, dominance, and evenness of the microbial communities.  The utilization of amino acid, amine, and carboxylic acid carbon sources and community evenness were further improved when the organic fertilizer amount was doubled in both years.  Biplot analysis indicated that amines and amino acids were the most representative of the total carbon source utilization by the soil microbial communities in both years.  The highest oat yield was achieved at a total N application rate of 135 kg ha–1 in the treatment involving 45 kg ha–1 N in the form of urea and 90 kg ha–1 N in the form of sheep manure in both years.  It was concluded that the application of 50% of the conventional rate of mineral N fertilizer supplemented with an appropriate rate of organic fertilizer enhanced both the functional diversity of soil microbial communities and oat yield.  Amine and amino acid carbon sources may be used as a substitute for total carbon sources for assessing total carbon source utilization by soil microbial communities in oat fields in future studies.
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    Effects of long-term straw incorporation on nematode community composition and metabolic footprint in a rice–wheat cropping system
    CHEN Yun-feng, XIA Xian-ge, HU Cheng, LIU Dong-hai, QIAO Yan, LI Shuang-lai, FAN Xian-peng
    2021, 20 (8): 2265-2276.   DOI: 10.1016/S2095-3119(20)63435-9
    Abstract88)      PDF in ScienceDirect      
    Soil nematode communities can provide valuable information about the structure and functions of soil food webs, and are sensitive to agricultural practices, including short-term straw incorporation.  However, currently, such effects under long-term straw incorporation conditions at different fertility levels are largely unknown.  Thus, we conducted a 13-year ongoing experiment to evaluate the effects of long-term straw incorporation on the structure and functions of the soil food web in low and high fertility soils through analyzing its effects on nematode communities, food web indices and metabolic footprints.  Four treatments were included: straw removal (–S) under non-fertilized (–NPK) or fertilized (+NPK) conditions; and straw incorporation (+S) under –NPK or +NPK conditions.  Soil samples from a 0–20 cm depth layer were collected when wheat and rice were harvested.  Compared with straw removal, straw incorporation increased the abundances of total nematodes, bacterivores, plant-parasites and omnivores-predators, as well the relative abundances of omnivores-predators with increases of 73.06, 89.29, 95.31, 238.98, and 114.61% in –NPK soils and 16.23, 2.23, 19.01, 141.38, and 90.23% in +NPK soils, respectively.  Regardless of sampling times and fertilization effects, straw incorporation increased the diversity and community stability of nematodes, as indicated by the Shannon-Weaver diversity index and maturity index.  Enrichment and structure index did not show significant responses to straw incorporation, but a slight increase was observed in the structure index.  The analysis of nematode metabolic footprints showed that straw incorporation increased the plant-parasite footprint and structure footprint by 97.27 and 305.39% in –NPK soils and by 11.29 and 149.56% in +NPK soils, but did not significantly influence enrichment, bacterivore and fungivore footprints.  In conclusion, long-term straw incorporation, particularly under a low fertility level, favored the soil nematodes and regulated the soil food web mainly via a top-down effect.   
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    The effects of soil properties, cropping systems and geographic location on soil prokaryotic communities in four maize production regions across China 
    TIAN Xue-liang, LIU Jia-jia, LIU Quan-cheng, XIA Xin-yao, PENG Yong, Alejandra I. HUERTA, YAN Jian-bing, LI Hui, LIU Wen-de
    2022, 21 (7): 2145-2157.   DOI: 10.1016/S2095-3119(21)63772-3
    Abstract111)      PDF in ScienceDirect      
    The diversity of prokaryotic communities in soil is shaped by both biotic and abiotic factors.  However, little is known about the major factors shaping soil prokaryotic communities at a large scale in agroecosystems.  To this end, we undertook a study to investigate the impact of maize production cropping systems, soil properties and geographic location (latitude and longitude) on soil prokaryotic communities using metagenomic techniques, across four distinct maize production regions in China.  Across all study sites, the dominant prokaryotes in soil were Alphaproteobacteria, Gammaproteobacteria, Betaproteobacteria, Gemmatimonadetes, Acidobacteria, and Actinobacteria.  Non-metric multidimensional scaling revealed that prokaryotic communities clustered into the respective maize cropping systems in which they resided.  Redundancy analysis (RDA) showed that soil properties especially pH, geographic location and cropping system jointly determined the diversity of the prokaryotic communities.  The functional genes of soil prokaryotes from these samples were chiefly influenced by latitude, soil pH and cropping system, as revealed by RDA analysis.  The abundance of genes in some metabolic pathways, such as genes involved in microbe–microbe interactions, degradation of aromatic compounds, carbon fixation pathways in prokaryotes and microbial metabolism were markedly different across the four maize production regions.  Our study indicated that the combination of soil pH, cropping system and geographic location significantly influenced the prokaryotic community and the functional genes of these microbes.  This work contributes to a deeper understanding of the composition and function of the soil prokaryotic community across large-scale production systems such as maize.

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    Increased ammonification, nitrogenase, soil respiration and microbial biomass N in the rhizosphere of rice plants inoculated with rhizobacteria
    ZHANG Jun-hua, HUANG Jing, Sajid HUSSAIN, ZHU Lian-feng, CAO Xiao-chuang, ZHU Chun-quan, JIN Qian-yu, ZHANG Hui
    2021, 20 (10): 2781-2796.   DOI: 10.1016/S2095-3119(20)63454-2
    Abstract81)      PDF in ScienceDirect      
    Azospirillum brasilense and Pseudomonas fluorescens are well-known plant growth promoting rhizobacteria.  However, the effects of A. brasilense and P. fluorescens on the N cycles in the paddy field and rice plant growth are little known.  This study investigated whether and how A. brasilense and P. fluorescens contribute to the N transformations and N supply capacities in the rhizosphere, and clarified the effects of A. brasilense and P. fluorescens on the N application rate in rice cultivation.  Inoculations with A. brasilense and P. fluorescens coupled with N application rate trials were conducted in the paddy field in 2016 and 2017.  The inoculations of rice seedlings included four treatments: sterile saline solution (M0), A. brasilense (Mb), P. fluorescens (Mp), and co-inoculation with a mixture of A. brasilense and P. fluorescens (Mbp).  The N application rate included four levels: 0 kg N ha–1 (N0), 90 kg N ha–1 (N90), 180 kg N ha–1 (N180), and 270 kg N ha–1 (N270).  The results indicated that the Mbp and Mp treatments significantly enhanced the ammonification activities in the rhizosphere compared with the M0 treatment, especially for higher N applications, while the Mbp and Mb treatments greatly enhanced the nitrogenase activities in the rhizosphere compared with the M0 treatments, especially for lower N applications.  Azospirillum brasilense and P. fluorescens did not participate in the nitrification processes or the denitrification processes in the soil.  The soil respiration rate and microbial biomass N were greatly affected by the interactions between the rhizobacteria inoculations and the N fertilizer applications.  In the Mbp treatment, N supply capacities and rice grain yields showed no significant differences among the N90, N180, and N270 applications.  The N application rate in the study region can be reduced to 90 kg N ha–1 for  rice seedlings co-inoculated with a mixture of A. brasilense and P. fluorescens.
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    Bacterial diversity and community composition changes in paddy soils that have different parent materials and fertility levels
    MA Xin-ling, LIU Jia, CHEN Xiao-fen, LI Wei-tao, JIANG Chun-yu, WU Meng, LIU Ming, LI Zhong-pei
    2021, 20 (10): 2797-2806.   DOI: 10.1016/S2095-3119(20)63364-0
    Abstract77)      PDF in ScienceDirect      
    Parent materials and the fertility levels of paddy soils are highly variable in subtropical China.  Bacterial diversity and community composition play pivotal roles in soil ecosystem processes and functions.  However, the effects of parent material and fertility on bacterial diversity and community composition in paddy soils are unclear.  The key soil factors driving the changes in bacterial diversity, community composition, and the specific bacterial species in soils that are derived from different parent materials and have differing fertility levels are unknown.  Soil samples were collected from paddy fields in two areas with different parent materials (quaternary red clay or tertiary sandstone) and two levels of fertility (high or low).  The variations in bacterial diversity indices and communities were evaluated by 454 pyrosequencing which targeted the V4–V5 region of the 16S rRNA gene.  The effects of parent material and fertility on bacterial diversity and community composition were clarified by a two-way ANOVA and a two-way PERMANOVA.  A principal coordinate analysis (PCoA), a redundancy analysis (RDA), and multivariate regression trees (MRT) were used to assess changes in the studied variables and identify the factors affecting bacterial community composition.  Co-occurrence network analysis was performed to find correlations between bacterial genera and specific soil properties, and a statistical analysis of metagenomic profiles (STAMP) was used to determine bacterial genus abundance differences between the soil samples.  The contributions made by parent material and soil fertility to changes in the bacterial diversity indices were comparable, but soil fertility accounted for a larger part of the shift in bacterial community composition than the parent material.  Soil properties, especially soil texture, were strongly associated with bacterial diversity.  The RDA showed that soil organic carbon (SOC) was the primary factor influencing bacterial community composition.  A key threshold for SOC (25.5 g kg–1) separated low fertility soils from high fertility soils.  The network analysis implied that bacterial interactions tended towards cooperation and that copiotrophic bacteria became dominant when the soil environment improved.  The STAMP revealed that copiotrophic bacteria, such as Massilia and Rhodanobacter, were more abundant in the high fertility soils, while oligotrophic bacteria, such as Anaerolinea, were dominant in low fertility soils.  The results showed that soil texture played a role in bacterial diversity, but nutrients, especially SOC, shaped bacterial community composition in paddy soils with different parent materials and fertility levels.
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    Modification of total and phosphorus mineralizing bacterial communities associated with Zea mays L. through plant development and fertilization regimes
    XIN Yuan-yuan, Anisur RAHMAN, LI Hui-xiu, XU Ting, DING Guo-chun, LI Ji
    2021, 20 (11): 3026-3038.   DOI: 10.1016/S2095-3119(20)63413-X
    Abstract56)      PDF in ScienceDirect      
    Harnessing the rhizospheric microbiome, including phosphorus mineralizing bacteria (PMB), is a promising technique for maintaining sustainability and productivity in intensive agricultural systems.  However, it is unclear as to which beneficial taxonomic group populations in the rhizosphere are potentially associated with the changes in soil microbiomes shifted by fertilization regimes.  Herein, we analyzed the diversity and community structure of total bacteria and PMB in the rhizosphere of maize (Zea mays L.) grown in soils under 25 years of four fertilization regimes (compost, biocompost, chemical, or non-fertilized) via selective culture and Illumina sequencing of the 16S rRNA genes.  Plant development explained more variations (29 and 13%, respectively) in the composition of total bacteria and PMB in the rhizosphere of maize than the different fertilization regimes.  Among those genera enriched in the rhizosphere of maize, the relative abundances of Oceanobacillus, Bacillus, Achromobacter, Ensifer, Paracoccus, Ramlibacter, and Luteimonas were positively correlated with those in the bulk soil.  The relative abundance of Paracoccus was significantly higher in soils fertilized by compost or biocompost than the other soils.  Similar results were also observed for PMB affiliated with Ensifer, Bacillus, and Streptomyces.  Although plant development was the major factor in shaping the rhizospheric microbiome of maize, fertilization regimes might have modified beneficial rhizospheric microbial taxa such as Bacillus and Ensifer
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    Linking changes in the soil microbial community to C and N dynamics during crop residue decomposition
    2021, 20 (11): 3039-3059.   DOI: 10.1016/S2095-3119(20)63567-5
    Abstract52)      PDF in ScienceDirect      
    Crop residues are among the main inputs that allow the organic carbon (C) and nutrients to be maintained in agricultural soil.  It is an important management strategy that can improve soil fertility and enhance agricultural productivity.  This work aims to evaluate the extent of the changes that may occur in the soil heterotrophic microbial communities involved in organic matter decomposition and C and nitrogen (N) mineralization after the addition of crop residues.  Soil microcosm experiments were performed at 28°C for 90 days with the addition of three crop residues with contrasting biochemical qualities: pea (Pisum sativum L.), rapeseed (Brassica napus L.), and wheat (Triticum aestivum L.).  Enzyme activities, C and N mineralization, and bacterial and fungal biomasses were monitored, along with the bacterial and fungal community composition, by the high-throughput sequencing of 16S rRNA and ITS genes.  The addition of crop residues caused decreases in β-glucosidase and arylamidase activities and simultaneous enhancement of the C mineralization and net N immobilization, which were linked to changes in the soil microbial communities.  The addition of crop residues decreased the bacterial and fungal biomasses 90 days after treatment and there were shifts in bacterial and fungal diversity at the phyla, order, and genera levels.  Some specific orders and genera were dependent on crop residue type.  For example, Chloroflexales, Inquilinus, Rubricoccus, Clitocybe, and Verticillium were identified in soils with pea residues; whereas Thermoanaerobacterales, Thermacetogenum, and Hypoxylon were enriched in soils with rapeseed residues, and Halanaerobiales, Rubrobacter, and Volutella were only present in soils with wheat residues.  The findings of this study suggest that soil C and N dynamics in the presence of the crop residues were driven by the selection of specific bacterial and fungal decomposers linked to the biochemical qualities of the crop residues.  If crop residue decomposition processes showed specific bacterial and fungal operational taxonomic unit (OTU) signatures, this study also suggests a strong functional redundancy that exists among soil microbial communities.
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    Characteristics of maize residue decomposition and succession in the bacterial community during decomposition in Northeast China
    ZHAO Shi-cheng, Ignacio A. CIAMPITTI, QIU Shao-jun, XU Xin-peng, HE Ping
    2021, 20 (12): 3289-3298.   DOI: 10.1016/S2095-3119(20)63570-5
    Abstract76)      PDF in ScienceDirect      
    Microbes are decomposers of crop residues, and climatic factors and residue composition are known to influence microbial growth and community composition, which in turn regulate residue decomposition.  However, the succession of the bacterial community during residue decomposition in Northeast China is not well understood.  To clarify the property of bacterial community succession and the corresponding factors regulating this succession, bags containing maize residue were buried in soil in Northeast China in October, and then at different intervals over the next 2 years, samples were analyzed for residue mass and bacterial community composition.  After residue burial in the soil, the cumulative residue mass loss rates were 18, 69, and 77% after 5, 12, and 24 months, respectively.  The release of residue nitrogen, phosphorus, and carbon followed a similar pattern as mass loss, but 79% of residue potassium was released after only 1 month.  The abundance, richness, and community diversity of bacteria in the residue increased rapidly and peaked after 9 or 20 months.  Residue decomposition was mainly influenced by temperature and chemical composition in the early stage, and was influenced by chemical composition in the later stage.  Phyla Actinobacteria, Bacteroidetes, and Firmicutes dominated the bacterial community composition in residue in the early stage, and the abundances of phyla Chloroflexi, Acidobacteria, and Saccharibacteria gradually increased in the later stage of decomposition.  In conclusion, maize residue decomposition in soil was greatly influenced by temperature and residue composition in Northeast China, and the bacterial community shifted from dominance of copiotrophic populations in the early stage to an increase in oligotrophic populations in the later stage. 
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    Assembly and co-occurrence patterns of rare and abundant bacterial sub-communities in rice rhizosphere soil under short-term nitrogen deep placement
    LI Gui-long, WU Meng, LI Peng-fa, WEI Shi-ping, LIU Jia, JIANG Chun-yu, LIU Ming, LI Zhong-pei
    2021, 20 (12): 3299-3311.   DOI: 10.1016/S2095-3119(20)63462-1
    Abstract71)      PDF in ScienceDirect      
    Nitrogen (N) deep placement has been found to reduce N leaching and increase N use efficiency in paddy fields.  However, relatively little is known how bacterial consortia, especially abundant and rare taxa, respond to N deep placement, which is critical for understanding the biodiversity and function of agricultural ecosystem.  In this study, Illumina sequencing and ecological models were conducted to examine the diversity patterns and underlying assembly mechanisms of abundant and rare taxa in rice rhizosphere soil under different N fertilization regimes at four rice growth stages in paddy fields.  The results showed that abundant and rare bacteria had distinct distribution patterns in rhizosphere samples.  Abundant bacteria showed ubiquitous distribution; while rare taxa exhibited uneven distribution across all samples.  Stochastic processes dominated community assembly of both abundant and rare bacteria, with dispersal limitation playing a more vital role in abundant bacteria, and undominated processes playing a more important role in rare bacteria.  The N deep placement was associated with a greater influence of dispersal limitation than the broadcast N fertilizer (BN) and no N fertilizer (NN) treatments in abundant and rare taxa of rhizosphere soil; while greater contributions from homogenizing dispersal were observed for BN and NN in rare taxa.  Network analysis indicated that abundant taxa with closer relationships were  usually more likely to occupy the central position of the network than rare taxa.  Nevertheless, most of the keystone species were rare taxa and might have played essential roles in maintaining the network stability.  Overall, these findings highlighted that the ecological mechanisms and co-occurrence patterns of abundant and rare bacteria in rhizosphere soil under N deep placement.
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    Fertility and biochemical activity in sodic soils 17 years after reclamation with flue gas desulfurization gypsum
    ZHAO Yong-gan, WANG Shu-juan, LIU Jia, ZHUO Yu-qun, LI Yan, ZHANG Wen-chao
    2021, 20 (12): 3312-3321.   DOI: 10.1016/S2095-3119(20)63446-3
    Abstract40)      PDF in ScienceDirect      
    Previous studies have mainly focused on changes in soil physical and chemical properties to evaluate the reclamation of sodic soils using flue gas desulfurization (FGD) gypsum.  However, information on the effects of this reclamation method on microbial-based indicators of soil quality is limited, particularly after many years of FGD gypsum application.  This study aimed to investigate the long-term effects of FGD gypsum on soil organic carbon (SOC), nutrients, microbial biomass and enzyme activity.  Data were collected from soils of three exchangeable sodium percentage (ESP) classes (i.e., low-, middle- and high-ESP classes of 6.1–20, 20–30 and 30–78.4%, respectively) 17 years after FGD gypsum treatment in Inner Mongolia, China.  Averaged across the three ESP classes, FGD gypsum application increased the SOC contents at the 0–20 and 20–40-cm soil depths by 18 and 35%, respectively, and increased available potassium at the 0–20-cm soil depth by 51% compared with the no-gypsum controls.  The microbial biomass carbon and microbial biomass nitrogen contents at the 20–40-cm soil depth increased by 69 and 194%, respectively, under FGD gypsum.  Except in the high-ESP class, urease activities in the 0–40 cm soil profile were significantly higher in the FGD gypsum treatments than in the controls.  A significant increase in alkaline phosphatase activity was concentrated in the 20–40 cm soil layer; few classes showed significant increases in catalase and invertase activities in the 0–20 cm soil layer.  Pearson correlation analysis showed that increases in soil fertility and biological activity could be attributed to reductions in electrical conductivity, pH and ESP caused by FGD gypsum application.  These results confirm that FGD gypsum application is a viable strategy for reclaiming sodic soils due to its positive effects on soil fertility and biochemistry and that it may contribute to soil ecosystem sustainability.
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    Preparation and efficacy evaluation of Paenibacillus polymyxa KM2501-1 microbial organic fertilizer against root-knot nematodes
    CHENG Wan-li, ZENG Li, YANG Xue, HUANG Dian, YU Hao, CHEN Wen, CAI Min-min, ZHENG Long-yu, YU Zi-niu, ZHANG Ji-bin
    2022, 21 (2): 542-551.   DOI: 10.1016/S2095-3119(20)63498-0
    Abstract97)      PDF in ScienceDirect      
    Root-knot nematodes (RKNs) cause huge yield losses to agricultural crops worldwide.  Meanwhile, livestock manure is often improperly managed by farmers, which leads to serious environmental pollution.  To resolve these two problems, this study developed a procedure for the conversion of chicken manure to organic fertilizer by larvae of Hermetia illucens L. and Bacillus subtilis BSF-CL.  Chicken manure organic fertilizer was then mixed thoroughly with Paenibacillus polymyxa KM2501-1 to a final concentration of 1.5×108 CFU g–1.  The efficacy of KM2501-1 microbial organic fertilizer in controlling root-knot nematodes was evaluated in pot and field experiments.  In pot experiments, applying KM2501-1 microbial organic fertilizer either as a base fertilizer or as a fumigant at the dose of 40 g/pot suppressed root-knot disease by 61.76 and 69.05% compared to the corresponding control treatments, respectively.  When applied as a fumigant at the dose of 1 kg m–2 in field experiments, KM2501-1 microbial organic fertilizer enhanced the growth of tomato plants, suppressed root-knot disease by 49.97%, and reduced second stage juveniles of RKN in soil by 88.68%.  KM2501-1 microbial organic fertilizer controlled RKNs better than commercial bio-organic fertilizer in both pot and field experiments.  These results demonstrate that this co-conversion process efficiently transforms chicken manure into high value-added larvae biomass and KM2501-1 microbial organic fertilizer with potential application as a novel nematode control agent.

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    Indigenous arbuscular mycorrhizal fungi play a role in phosphorus depletion in organic manure amended high fertility soil
    HUO Wei-ge, CHAI Xiao-fen, WANG Xi-he, William David BATCHELOR, Arjun KAFLE, FENG Gu
    2022, 21 (10): 3051-3066.   DOI: 10.1016/j.jia.2022.07.045
    Abstract337)      PDF in ScienceDirect      

    The species richness and propagule number of arbuscular mycorrhizal fungi (AMF) are high in intensively-managed agricultural soils.  Past research has shown that AMF improve crop phosphorus (P) uptake under low soil P conditions, however it is unclear if AMF play a role in high Olsen-P soils.  In this study, we investigated whether native fungal benefits exist under high P input field conditions in-situ and contribute to P utilization.  We installed in-grow tubes which were sealed with different membrane pore sizes (30 or 0.45 µm) to allow or prevent AMF hyphae access to the hyphal compartment and prevent cotton roots from penetrating the chamber.  We used the depletion of soil available P (Olsen-P) in the hyphae accessed compartment to indicate P uptake by the native AMF community.  Our results showed that the native AMF mediated P depletion and microbial biomass P (MBP) turnover and caused the largest Olsen-P depletion ratio and MBP turnover ratio in the high P treatments (Olsen-P: 78.29 mg kg–1).  The cotton roots in each fertilization regime were colonized by a unique AMF community and Glomus and Paraglomus were the dominant genera, implying the long-term fertilization regimes domesticated the AMF community.  We conclude that native AMF caused the P depletion and P turnover even under high soil Olsen-P conditions.

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