Small farm holder cropping systems, datasets

File descriptions:dada2_workflow_1.4.R - R DADA2 workflow to process raw fastq datadada2_sv_seqs.xlsx - FASTA sequence file from DADA2 outputdada2_readsout.xlsx - ASV table from DADA2 outputMatindu_physico_chemical_data.xlsx - table of soil dataMatindu_SV.xlsx - file of edited raw DADA2 data, for input into Rfigures.R - R code for analysis using Matindu_SV.xlsx sheets as inputPlease see ENA project accession PRJEB44367 for raw FASTQ data.<b>Abstract.</b> Metabarcoding of prokaryotic and fungal ribosomal DNA was used to describe the microbial communities in soils of remnant equatorial rainforest, maize-bean intercrop, and sugarcane in western Kenya. Cropping systems influenced the microbial community composition and functional traits (energy source and nutrient cycling) of bulk soil in each crop. Microbial richness and diversity tended to increase with cultivation intensity. Soil of maize-bean intercrop had lower percentages and sugarcane had higher percentages of unique amplicon sequence variants of both bacteria and fungi compared to the remnant forest. Functional traits were altered by cultivation intensity. Compared to remnant forest soils, maize-bean intercrop soil had lower percentages of aerobic chemoheterotrophic bacteria and higher percentages of N-cycling bacteria, while sugarcane had higher percentages of aerobic chemoheterotrophic bacteria and lower percentages of N-cycling bacteria. In the face of increasing forest loss and pressures for agricultural productivity, this landscape provides a rich site for studying the impacts of cropping systems on soil health.文件说明： dada2_workflow_1.4.R：用于处理原始FASTQ数据的R语言DADA2分析工作流 dada2_sv_seqs.xlsx：来自DADA2分析结果的FASTA序列文件 dada2_readsout.xlsx：来自DADA2分析结果的扩增子序列变异（Amplicon Sequence Variant）表 Matindu_physico_chemical_data.xlsx：土壤理化特性数据表 Matindu_SV.xlsx：经过编辑的原始DADA2数据文件，可作为R语言分析的输入数据 figures.R：以Matindu_SV.xlsx的工作表作为输入开展数据分析的R代码 如需获取原始FASTQ数据，请查阅ENA项目登录号PRJEB44367。 【摘要】本研究通过对原核生物与真菌核糖体DNA开展元条形码测序（Metabarcoding），对肯尼亚西部残存赤道热带雨林、玉米-豆科作物间作田以及甘蔗田的土壤微生物群落进行解析。种植制度会影响各作物田块中非根际土壤的微生物群落组成及其功能性状（涵盖能源源与养分循环功能）。微生物丰富度与多样性往往随耕作强度的提升而升高。与残存热带雨林土壤相比，玉米-豆科间作田土壤中的细菌与真菌特有扩增子序列变异占比更低，而甘蔗田土壤的该类变异占比更高。功能性状会随耕作强度发生改变。与残存热带雨林土壤相比，玉米-豆科间作田土壤中的有氧化能异养细菌占比更低，氮循环细菌占比更高；而甘蔗田土壤则呈现相反趋势，其有氧化能异养细菌占比更高，氮循环细菌占比更低。面对日益加剧的森林丧失与农业生产压力，该研究区域为探究种植制度对土壤健康的影响提供了极佳的研究场景。