There is an urgent need for novel agronomic improvements capable of boosting crop yields while alleviating environmental impacts. One such approach is the use of optimized crop rotations. However, a set of measurements that can serve as guiding principles for the design of crop rotations is lacking. Crop rotations take advantage of niche complementarity, enabling the optimization of nutrient use and the reduction of pests and specialist pathogen loads. However, despite the recognized importance of plant-soil microbial interactions and feedbacks for crop yield and soil health, this is ignored in the selection and management of crops for rotation systems. We review the literature and propose criteria for the design of crop rotations focusing on the roles of soil biota and feedback on crop productivity and soil health. We consider that identifying specific key organisms or consortia capable of influencing plant productivity is more important as a predictor of soil health and crop productivity than assessing the overall soil microbial diversity per se. As such, we propose that setting up soil feedback studies and applying genetic sequencing tools towards the development of soil biotic community databases has a strong potential to enable the establishment of improved soil health indicators for optimized crop rotations.© 2014 Society of Chemical Industry.

不同种植模式具有不同的经济学和生态学意义,因地制宜确立合理的种植模式是保护黑土地的重要措施。目前,对东北黑土区的种植模式类型及其空间格局尚缺乏系统的认识。本研究基于东北黑土区2017—2019年作物分类数据,应用地学信息图谱理论和方法构建种植模式图谱,以揭示黑土区种植模式类型及其空间格局,并在此基础上使用分布指数模型和双变量空间自相关方法分析了种植模式的分布规律。结果表明: 1) 东北黑土区种植模式主要有玉米连作、水稻连作、大豆连作和米(玉米)豆(大豆)轮作,面积占比分别为38.3%、18.5%、10.3%、26.0%。其中,米豆轮作又包括米豆两年轮作、米米豆三年轮作、豆豆米三年轮作,分别占轮作面积的44.1%、34.5%、21.4%;2) 各类种植模式的水平地带性分异规律显著。其中,玉米连作在温度和湿度上的梯度分异特征均非常明显,水稻连作仅在湿度上的梯度分异特征非常明显,大豆连作和米豆轮作在温度和湿度上的梯度分异特征均不明显;3) 各类种植模式的空间集聚特征显著,种植模式间存在“大豆连作→豆豆米三年轮作→米豆两年轮作→米米豆三年轮作→玉米连作”的空间过渡特征。东北黑土区种植模式以连作为主,其分布规律可为今后轮作空间优化提供依据。

Biodiversity loss, an important consequence of agricultural intensification, can lead to reductions in agroecosystem functions and services. Increasing crop diversity through rotation may alleviate these negative consequences by restoring positive aboveground-belowground interactions. Positive impacts of aboveground biodiversity on belowground communities and processes have primarily been observed in natural systems. Here, we test for the effects of increased diversity in an agroecosystem, where plant diversity is increased over time through crop rotation. As crop diversity increased from one to five species, distinct soil microbial communities were related to increases in soil aggregation, organic carbon, total nitrogen, microbial activity and decreases in the carbon-to-nitrogen acquiring enzyme activity ratio. This study indicates positive biodiversity-function relationships in agroecosystems, driven by interactions between rotational and microbial diversity. By increasing the quantity, quality and chemical diversity of residues, high diversity rotations can sustain soil biological communities, with positive effects on soil organic matter and soil fertility. © 2015 John Wiley & Sons Ltd/CNRS.

Exserohilum rostratum was the major cause of an outbreak of fungal infections linked to injections of contaminated methylprednisolone acetate. Because almost 14,000 persons were exposed to product that was possibly contaminated with multiple fungal pathogens, there was unprecedented need for a rapid throughput diagnostic test that could detect both E. rostratum and other unusual agents of fungal infection. Here we report development of a novel PCR test that allowed for rapid and specific detection of fungal DNA in cerebrospinal fluid (CSF), other body fluids and tissues of infected individuals. The test relied on direct purification of free-circulating fungal DNA from fluids and subsequent PCR amplification and sequencing. Using this method, we detected Exserohilum rostratum DNA in 123 samples from 114 case-patients (28% of 413 case-patients for whom 627 samples were available), and Cladosporium DNA in one sample from one case-patient. PCR with novel Exserohilum-specific ITS-2 region primers detected 25 case-patients with samples that were negative using broad-range ITS primers. Compared to fungal culture, this molecular test was more sensitive: of 139 case-patients with an identical specimen tested by culture and PCR, E. rostratum was recovered in culture from 19 (14%), but detected by PCR in 41 (29%), showing a diagnostic sensitivity of 29% for PCR compared to 14% for culture in this patient group. The ability to rapidly confirm the etiologic role of E. rostratum in these infections provided an important contribution in the public health response to this outbreak.

The rhizosphere is of central importance not only for plant nutrition, health and quality but also for microorganism-driven carbon sequestration, ecosystem functioning and nutrient cycling in terrestrial ecosystems. A multitude of biotic and abiotic factors are assumed to influence the structural and functional diversity of microbial communities in the rhizosphere. In this review, recent studies on the influence of the two factors, plant species and soil type, on rhizosphere-associated microbial communities are discussed. Root exudates and the response of microorganisms to the latter as well as to root morphology were shown to shape rhizosphere microbial communities. All studies revealed that soil is the main reservoir for rhizosphere microorganisms. Many secrets of microbial life in the rhizosphere were recently uncovered due to the enormous progress in molecular and microscopic tools. Physiological and molecular data on the factors that drive selection processes in the rhizosphere are presented here. Furthermore, implications for agriculture, nature conservation and biotechnology will also be discussed.

Intercropping plays a vital role in greenhouse production, and affects soil physicochemical properties and soil microbial communities structure, but influences of intercropping on the relationship of microorganisms are reported in continuous cropping soil rarely. Here, we investigated the effects of seven intercropping systems [alfalfa (Medicago sativa L.)/cucumber, trifolium (Trifolium repens L.)/cucumber, wheat (Triticum aestivum L.)/cucumber, rye (Secale cereale L.)/cucumber, chrysanthemum (Chrysanthemum coronrium L.)/cucumber, rape (Brassica campestris L.)/cucumber, mustard (Brassica juncea L.)/cucumber] on soil bacterial and fungal communities compared to the cucumber continuous cropping system in the greenhouse. The results showed that intercropping increased microbial OTU richness and fungal communities diversity, soil bacterial communities diversity was abundant in the trifolium-cucumber and mustard-cucumber systems. Nevertheless, there was no significant differences of microbial communities structure between intercropping and monoculture systems. Redundancy analysis indicated that soil microbial communities composition was indirectly influenced by soil properties. In addition, network analysis demonstrated that simple inter-relationships of fungal taxa were observed in the intercropping soil, and trifolium, wheat, and mustard intercropping systems had a complex connection between bacterial taxa. Taken together, trifolium and mustard as the intercrops significantly increased cucumber continuous cropping soil bacterial and fungal communities diversity. Moreover, intercropping strongly changed the relationships of microbial taxa, though did not shape notably soil microbial communities structure.

We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.

The phylum Ascomycota is by far the largest group in the fungal kingdom. Ecologically important mutualistic associations such as mycorrhizae and lichens have evolved in this group, which are regarded as key innovations that supported the evolution of land plants. Only a few attempts have been made to date the origin of Ascomycota lineages by using molecular clock methods, which is primarily due to the lack of satisfactory fossil calibration data. For this reason we have evaluated all of the oldest available ascomycete fossils from amber (Albian to Miocene) and chert (Devonian and Maastrichtian). The fossils represent five major ascomycete classes (Coniocybomycetes, Dothideomycetes, Eurotiomycetes, Laboulbeniomycetes, and Lecanoromycetes). We have assembled a multi-gene data set (18SrDNA, 28SrDNA, RPB1 and RPB2) from a total of 145 taxa representing most groups of the Ascomycota and utilized fossil calibration points solely from within the ascomycetes to estimate divergence times of Ascomycota lineages with a Bayesian approach. Our results suggest an initial diversification of the Pezizomycotina in the Ordovician, followed by repeated splits of lineages throughout the Phanerozoic, and indicate that this continuous diversification was unaffected by mass extinctions. We suggest that the ecological diversity within each lineage ensured that at least some taxa of each group were able to survive global crises and rapidly recovered. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

高温真菌特异腐质霉（Humicola insolens）具有强大的纤维素酶分泌和纤维素降解能力，因此在生物质能源、饲料和纺织工业等领域中具有良好的应用前景。在特异腐质霉T-DNA随机插入突变体库中筛选得到一株纤维素酶高产菌株T53。在纤维素诱导培养条件下，突变株T53发酵上清中的滤纸酶活力、内切β-1,4葡聚糖酶活力、纤维二糖水解酶活力、β-葡萄糖苷酶活力以及木聚糖酶活力较野生型菌株分别提高了40%、60%、90%、10%、60%。蛋白电泳结果显示，T53菌株的胞外总蛋白特别是纤维素酶与半纤维素酶的分泌量较野生型菌株有显著提高。TAIL-PCR克隆鉴定了T53菌株中的T-DNA插入位点侧翼序列，结果表明T-DNA插入位点位于一个可能的C2H2型锌指蛋白类转录因子编码基因的上游启动子区域。这为揭示突变株T53中纤维素酶的高产分子机制奠定了重要基础，有助于理解特异腐质霉中纤维素酶的表达调控机制，为特异腐质霉纤维素酶高产工程菌的构建奠定了理论和技术基础。