Karapareddy Sowndarya, Anche Varsha C, Tamatamu Sowjanya R, Janga Madhusudhana R, Lawrence Kathy, Nyochembeng Leopold M, Todd Antonette, Walker Lloyd T, Sripathi Venkateswara R
College of Agricultural, Life & Natural Sciences, Alabama A&M University, Normal, AL, United States.
Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States.
Front Plant Sci. 2025 Mar 7;16:1521579. doi: 10.3389/fpls.2025.1521579. eCollection 2025.
Plant roots, nematodes, and soil microorganisms have a complex interaction in the rhizosphere by exchanging or communicating through biomolecules or chemicals or signals. Some rhizospheric (including endophytic) microbes process such compounds via biogeochemical cycles to improve soil fertility, promote plant growth and development, and impart stress tolerance in plants. Some rhizospheric microbes can affect negatively on plant parasitic nematodes (PPNs) thus hindering the ability of nematodes in parasitizing the plant roots. Next-generation sequencing is one of the most widely used and cost-effective ways of determining the composition and diversity of microbiomes in such complex environmental samples.
This study employed amplicon sequencing (Illumina/NextSeq) of 16S ribosomal RNA (16S rRNA) for bacteria and Internal Transcribed Spacer (ITS2) region for fungi to profile the soil microbiome in the rhizosphere of cotton grown in North Alabama. We isolated DNA (ZymoBIOMICS) from soil samples in triplicates from four representative locations of North Alabama. Based on the level of Reniform Nematode (RN) Infestation, these locations were classified as Group A-RN Not-Detected (ND), Group B-RN Low Infestation (LI), Group C-RN Medium Infestation (MI), and Group D-RN High Infestation (HI) and determined using sieving method and microscopic examination.
Our analyses identified 47,893 bacterial and 3,409 fungal Amplicon Sequence Variants (ASVs) across all groups. Among the bacterial ASVs, 12,758, 10,709, 12,153, and 11,360 unique ASVs were determined in Groups A, B, C, and D, respectively. While 663, 887, 480, and 326 unique fungal ASVs were identified in Groups A, B, C, and D, respectively. Also, the five most abundant rhizospheric bacterial genera identified were , , , , . Moreover, five abundant fungal genera belonging to were identified. The tight clustering of bacterial nodes in , , and shows they are highly similar and often found together. On the other hand, the close association of and suggesting that they have different ecological roles but occupy similar niches and contribute similar functions within the microbial community. The abundant microbial communities identified in this study had a role in nutrient recycling, soil health, plant resistance to some environmental stress and pests including nematodes, and biogeochemical cycles. Our findings will aid in broadening our understanding of how microbial communities interact with crops and nematodes in the rhizosphere, influencing plant growth and pest management.
植物根系、线虫和土壤微生物通过生物分子、化学物质或信号进行交换或交流，在根际存在复杂的相互作用。一些根际（包括内生）微生物通过生物地球化学循环处理此类化合物，以提高土壤肥力、促进植物生长发育并赋予植物抗逆性。一些根际微生物会对植物寄生线虫（PPN）产生负面影响，从而阻碍线虫寄生植物根系的能力。下一代测序是确定此类复杂环境样本中微生物群落组成和多样性最广泛使用且经济高效的方法之一。
本研究采用对细菌的16S核糖体RNA（16S rRNA）和对真菌的内转录间隔区（ITS2）区域进行扩增子测序（Illumina/NextSeq），以分析阿拉巴马州北部种植的棉花根际土壤微生物群落。我们从阿拉巴马州北部四个代表性地点的土壤样本中一式三份地分离DNA（ZymoBIOMICS）。根据肾形线虫（RN）侵染水平，这些地点被分为A组 - RN未检测到（ND）、B组 - RN低侵染（LI）、C组 - RN中度侵染（MI）和D组 - RN高侵染（HI），并通过筛分法和显微镜检查确定。
我们的分析在所有组中鉴定出47,893个细菌扩增子序列变体（ASV）和3,409个真菌ASV。在细菌ASV中，A组、B组、C组和D组分别确定了12,758、10,709、12,153和11,360个独特的ASV。而A组、B组、C组和D组分别鉴定出663、887、480和326个独特的真菌ASV。此外，确定的五个最丰富的根际细菌属为 ， ， ， ， 。此外，鉴定出了属于 的五个丰富真菌属。 、 和 中细菌节点的紧密聚类表明它们高度相似且经常一起出现。另一方面， 和 的紧密关联表明它们具有不同的生态作用，但占据相似的生态位并在微生物群落中发挥相似的功能。本研究中鉴定出的丰富微生物群落具有营养循环、土壤健康、植物对包括线虫在内的一些环境胁迫和害虫的抗性以及生物地球化学循环等作用。我们的研究结果将有助于拓宽我们对微生物群落在根际如何与作物和线虫相互作用、影响植物生长和害虫管理的理解。
