Rojas J Alejandro, Jacobs Janette L, Napieralski Stephanie, Karaj Behirda, Bradley Carl A, Chase Thomas, Esker Paul D, Giesler Loren J, Jardine Doug J, Malvick Dean K, Markell Samuel G, Nelson Berlin D, Robertson Alison E, Rupe John C, Smith Damon L, Sweets Laura E, Tenuta Albert U, Wise Kiersten A, Chilvers Martin I
First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907.
Phytopathology. 2017 Mar;107(3):293-304. doi: 10.1094/PHYTO-04-16-0176-R. Epub 2017 Jan 18.
Soybean (Glycine max (L.) Merr.) is produced across a vast swath of North America, with the greatest concentration in the Midwest. Root rot diseases and damping-off are a major concern for production, and the primary causal agents include oomycetes and fungi. In this study, we focused on examination of oomycete species distribution in this soybean production system and how environmental and soil (edaphic) factors correlate with oomycete community composition at early plant growth stages. Using a culture-based approach, 3,418 oomycete isolates were collected from 11 major soybean-producing states and most were identified to genus and species using the internal transcribed spacer region of the ribosomal DNA. Pythium was the predominant genus isolated and investigated in this study. An ecology approach was taken to understand the diversity and distribution of oomycete species across geographical locations of soybean production. Metadata associated with field sample locations were collected using geographical information systems. Operational taxonomic units (OTU) were used in this study to investigate diversity by location, with OTU being defined as isolate sequences with 97% identity to one another. The mean number of OTU ranged from 2.5 to 14 per field at the state level. Most OTU in this study, classified as Pythium clades, were present in each field in every state; however, major differences were observed in the relative abundance of each clade, which resulted in clustering of states in close proximity. Because there was similar community composition (presence or absence) but differences in OTU abundance by state, the ordination analysis did not show strong patterns of aggregation. Incorporation of 37 environmental and edaphic factors using vector-fitting and Mantel tests identified 15 factors that correlate with the community composition in this survey. Further investigation using redundancy analysis identified latitude, longitude, precipitation, and temperature as factors that contribute to the variability observed in community composition. Soil parameters such as clay content and electrical conductivity also affected distribution of oomycete species. The present study suggests that oomycete species composition across geographical locations of soybean production is affected by a combination of environmental and edaphic conditions. This knowledge provides the basis to understand the ecology and distribution of oomycete species, especially those able to cause diseases in soybean, providing cues to develop management strategies.
大豆（Glycine max (L.) Merr.）在北美广大地区种植，其中中西部地区种植最为集中。根腐病和猝倒病是大豆生产中的主要问题，其主要致病因子包括卵菌和真菌。在本研究中，我们重点考察了大豆生产系统中卵菌物种的分布情况，以及环境和土壤（土壤学）因素在植物生长早期与卵菌群落组成的相关性。采用基于培养的方法，从11个主要大豆生产州收集了3418株卵菌分离株，并利用核糖体DNA的内部转录间隔区将大多数分离株鉴定到属和种。腐霉属是本研究中分离和研究的主要属。我们采用生态学方法来了解大豆生产不同地理位置上卵菌物种的多样性和分布。利用地理信息系统收集与田间样本位置相关的元数据。本研究中使用操作分类单元（OTU）来按位置调查多样性，OTU被定义为彼此具有97%同一性的分离株序列。在州一级，每个田间的OTU平均数在2.5到14之间。本研究中大多数归类为腐霉分支的OTU存在于每个州的每个田间；然而，观察到每个分支的相对丰度存在重大差异，这导致地理位置相近的州聚集在一起。由于州之间的群落组成（存在或不存在）相似，但OTU丰度存在差异，排序分析未显示出强烈的聚集模式。使用向量拟合和Mantel检验纳入37个环境和土壤学因素后，确定了15个与本次调查中的群落组成相关的因素。进一步使用冗余分析进行调查后发现，纬度、经度、降水量和温度是导致群落组成出现变异性的因素。土壤参数如粘土含量和电导率也影响卵菌物种的分布。本研究表明，大豆生产不同地理位置上的卵菌物种组成受环境和土壤条件的综合影响。这些知识为理解卵菌物种的生态学和分布提供了基础，特别是那些能够在大豆中致病的卵菌，为制定管理策略提供了线索。
