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1. JIA-2022-0138 再植桃园土壤微生物群落变化

LI Wei-hua, CHEN Peng, WANG Yu-zhu, LIU Qi-zhi

Journal of Integrative Agriculture 2023, 22 (4): 1082-1092. DOI: 10.1016/j.jia.2022.08.121

摘要（213）

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以不同年份再植桃园根系土壤为材料，探究再植桃园微生物群落结构的变化情况，并进一步揭示不同年份的再植桃园微生物群落和土壤养分之间的关系，以期为桃树再植病调控提供理论依据。分别收集非再植（NRS）和再植（RS）(再植1年RS1、再植3年RS3、再植5年RS5、再植7年RS7、再植9年RS9、再植11年RS11)桃园桃树的根际土壤，利用高通量测序技术测定土壤细菌和真菌群落的多样性，同时采用RDA分析土壤微生物群落与土壤环境因子之间的关系。结果显示，RS早期（1-5年）的土壤养分含量低于NRS，但随着桃树种植年限的增加，它们之间的差异逐渐缩小，直至达到相近的水平。细菌和真菌群落的alpha多样性指数表明，RS比NRS含有更高丰度的细菌和真菌OUT含量。NMDS和ANOSIM分析表明，土壤细菌和真菌群落显著受种植年限影响（p<0.01），其变化主要发生在种植1年和9年。从目的分类水平看，再植桃园土壤中，Sphingobacteriales, Burkholderiales 和 Actinomycetales显著发生变化。一些与生物修复相关的细菌，如Burkholderiales目和 Intrasporangiaceae纲，以及一些有害的病原真菌，如Penicillium属和 Ophiostomatales纲,在再植桃园中显着增加（LDA> 3.0）。此外， RDA结果表明微生物群落的组成与环境各因子（pH、AP、AN 和 AK）间存在密切相关。从细菌门的分类水平看，这些环境变量与Acidobacteria, Chloroflexi, 和 Actinobacteria呈正相关，与Proteobacteria 和 Firmicutes呈负相关。在真菌门水平中，Basidiomycota门在 pH、AP 和 AN 增加的环境中增强，而Ascomycota, Chytridiomycota 和 Zygomycota门与 AK 呈正相关。RS的细菌和真菌群落多样性高于NRS，桃树再植病害的发生与土壤微生物群落的变化密切相关。我们的研究结果详细阐明了不同年份的 NRS 和 RS微生物群落的变化情况以及两者之间土壤理化和微生物群落变化之间的关系。这些结果使人们更加深入的了解再植桃园微生物群落的变化，为桃树再植病的解决提供思路。

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2. Effect of long-term continuous cropping of strawberry on soil bacterial community structure and diversity

LI Wei-hua, LIU Qi-zhi, CHEN Peng

Journal of Integrative Agriculture 2018, 17 (11): 2570-2582. DOI: 10.1016/S2095-3119(18)61944-6

摘要（365）

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Long-term monoculture leads to continuous cropping (CC) problems, which complicate agricultural production, both locally and abroad. This study contrasted the different bacterial community compositions, physicochemical properties and enzyme activities of strawberry soil subjected to CC, CC rhizosphere (CCR), non-CC (NCC) and non-CC rhizosphere (NCCR) treatments. The soil physicochemical properties and enzyme activities were significantly reduced after long-term CC. In addition, five variation trends were observed for the 11 major bacterial genera in the soil. Sphingomonas was the only stable group among all treatments. The proportions of Novosphingobium, Rhodoplanes, Povalibacter, Cellvibrio and Stenotrophobacter decreased after CC. The relative abundances of Pelagibius, Thioprofundum and Allokutzneria increased only in the CC treatment. Nitrospira were more abundant in rhizosphere soil than in non-rhizosphere soil. The relative abundance of Bacillus increased after CC. Redundancy analysis revealed that Bacillus, Pelagibius and Allokutzneria had significant negative correlations with the soil physicochemical properties and enzyme activities. Therefore, these genera may be the key bacteria influenced by the physicochemical properties and enzyme activities altered by replanting. These results indicate that long-term CC of strawberry leads to less favourable rhizosphere soil conditions, which can be understood as a stress-induced response of the bacterial community diversity. Further research is needed to determine how the quality of soil is reduced by the shift in the diversity of the soil bacterial community.

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3. Effects of land use change on the spatiotemporal variability of soil organic carbon in an urban-rural ecotone of Beijing, China

YE Hui-chun, HUANG Yuan-fang, CHEN Peng-fei, HUANG Wen-jiang, ZHANG Shi-wen, HUANG Shan-yu, HOU Sen

Journal of Integrative Agriculture 2016, 15 (4): 918-928. DOI: 10.1016/S2095-3119(15)61066-8

摘要（1927）

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Understanding the effects of land use changes on the spatiotemporal variation of soil organic carbon (SOC) can provide guidance for low carbon and sustainable agriculture. In this paper, based on the large-scale datasets of soil surveys in 1982 and 2009 for Pinggu District — an urban-rural ecotone of Beijing, China, the effects of land use and land use changes on both temporal variation and spatial variation of SOC were analyzed. Results showed that from 1982 to 2009 in Pinggu District, the following land use change mainly occurred: Grain cropland converted to orchard or vegetable land, and grassland converted to forestland. The SOC content decreased in region where the land use type changed to grain cropland (e.g., vegetable land to grain cropland decreased by 0.7 g kg^–1; orchard to grain cropland decreased by 0.2 g kg^–1). In contrast, the SOC content increased in region where the land use type changed to either orchard (excluding forestland) or forestland (e.g., grain cropland to orchard and forestland increased by 2.7 and 2.4 g kg^–1, respectively; grassland to orchard and forestland increased by 4.8 and 4.9 g kg^–1, respectively). The organic carbon accumulation capacity per unit mass of the soil increased in the following order: grain cropland soil

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4. Recent Advances in the Role of the Elongator Complex in Plant Physiology and tRNA Modification: A Review

YAN Xu, JIN Xiao-huan, WANG You-mei, ZHENG Bo , CHEN Peng

Journal of Integrative Agriculture 2014, 13 (8): 1640-1650. DOI: 10.1016/S2095-3119(13)60524-9

摘要（1125）

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The Elongator complex is a multifunction protein complex which has been shown to be involved in transcriptional elongation, DNA replication and repair, tubulin and histone acetylation, gene silencing and tranfer RNA uridine modification. The composition of the Elongator complex is found to be highly conserved in eukaryotes, protein homologs of various subunits have been identified in fungi, plant, animal, and human. Remarkably, mutation in genes encoding the Elongator complex structural components all results in defects of transfer RNA wobble uridine modification, and this function of the Elongator complex is also conserved in eukaryotes. The Elongator complex mutants in higher plants have pleiotropic phenotypes including defects in vegetative growth, abiscisic acid hypersensitivity, elevated tolerance to drought and oxidative stress. What is the relationship between the Elongator complex’s function in nucleoside modification and its activity in other cellular pathways? This review summarizes the recent advances in study of function of the Elongator complex, in the aspects of cell physiology and molecular biology.

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5. Agricultural Ontology Based Feature Optimization for Agricultural Text Clustering

SU Ya-ru, WANG Ru-jing, CHEN Peng, WEI Yuan-yuan, LI Chuan-xi

Journal of Integrative Agriculture 2012, 11 (5): 752-759. DOI: 10.1016/S1671-2927(00)8596

摘要（1422）

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Feature optimization is important to agricultural text mining. Usually, the vector space model is used to represent text documents. However, this basic approach still suffers from two drawbacks: the curse of dimension and the lack of semantic information. In this paper, a novel ontology-based feature optimization method for agricultural text was proposed. First, terms of vector space model were mapped into concepts of agricultural ontology, which concept frequency weights are computed statistically by term frequency weights; second, weights of concept similarity were assigned to the concept features according to the structure of the agricultural ontology. By combining feature frequency weights and feature similarity weights based on the agricultural ontology, the dimensionality of feature space can be reduced drastically. Moreover, the semantic information can be incorporated into this method. The results showed that this method yields a significant improvement on agricultural text clustering by the feature optimization.

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