Caldwell Adam Collins, Silva Lívia Carneiro Fidéles, da Silva Cynthia Canêdo, Ouverney Cleber Costa
Department of Biological Sciences, San Jose State University, San Jose, California, 95192-0100, United States of America.
Department of Microbiology, Federal University of Viçosa, Viçosa, MG, 36570, Brazil.
PLoS One. 2015 Jun 17;10(6):e0106355. doi: 10.1371/journal.pone.0106355. eCollection 2015.
Despite a continuous rise in consumption of coffee over the past 60 years and recent studies showing positive benefits linked to human health, intensive coffee farming practices have been associated with environmental damage, risks to human health, and reductions in biodiversity. In contrast, organic farming has become an increasingly popular alternative, with both environmental and health benefits. This study aimed to characterize and determine the differences in the prokaryotic soil microbiology of three Brazilian coffee farms: one practicing intensive farming, one practicing organic farming, and one undergoing a transition from intensive to organic practices. Soil samples were collected from 20 coffee plant rhizospheres (soil directly influenced by the plant root exudates) and 10 control sites (soil 5 m away from the coffee plantation) at each of the three farms for a total of 90 samples. Profiling of 16S rRNA gene V4 regions revealed high levels of prokaryotic diversity in all three farms, with thousands of species level operational taxonomic units identified in each farm. Additionally, a statistically significant difference was found between each farm's coffee rhizosphere microbiome, as well as between coffee rhizosphere soils and control soils. Two groups of prokaryotes associated with the nitrogen cycle, the archaeal genus Candidatus Nitrososphaera and the bacterial order Rhizobiales were found to be abundant and statistically different in composition between the three farms and in inverse relationship to each other. Many of the nitrogen-fixing genera known to enhance plant growth were found in low numbers (e.g. Rhizobium, Agrobacter, Acetobacter, Rhodospirillum, Azospirillum), but the families in which they belong had some of the highest relative abundance in the dataset, suggesting many new groups may exist in these samples that can be further studied as potential plant growth-promoting bacteria to improve coffee production while diminishing negative environmental impacts.
尽管在过去60年里咖啡的消费量持续上升，且近期研究表明咖啡对人类健康有积极益处，但集约化咖啡种植方式却与环境破坏、人类健康风险以及生物多样性减少有关。相比之下，有机种植已成为越来越受欢迎的选择，它对环境和健康都有益处。本研究旨在描述和确定巴西三个咖啡农场原核土壤微生物学的特征及差异：一个采用集约化种植，一个采用有机种植，还有一个正从集约化种植向有机种植转变。在这三个农场的每个农场，从20个咖啡植株根际（直接受植物根系分泌物影响的土壤）和10个对照地点（距咖啡种植园5米处的土壤）采集土壤样本，共采集90个样本。对16S rRNA基因V4区域的分析表明，所有三个农场的原核生物多样性水平都很高，每个农场都鉴定出了数千个物种水平的操作分类单元。此外，还发现每个农场的咖啡根际微生物群之间，以及咖啡根际土壤和对照土壤之间存在统计学上的显著差异。发现与氮循环相关的两组原核生物，即古菌属的“暂定亚硝化球菌属（Candidatus Nitrososphaera）”和细菌目“根瘤菌目（Rhizobiales）”，在三个农场中含量丰富且组成在统计学上存在差异，并且彼此呈反比关系。许多已知能促进植物生长的固氮属数量较少（如根瘤菌属、土壤杆菌属、醋杆菌属、红螺菌属、固氮螺菌属），但其所属科在数据集中的相对丰度却处于最高水平，这表明这些样本中可能存在许多新的菌群，可作为潜在的促进植物生长的细菌进一步研究，以提高咖啡产量，同时减少负面环境影响。
