Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil.
Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, DF, Brazil.
Mol Ecol Resour. 2023 Jan;23(1):64-80. doi: 10.1111/1755-0998.13690. Epub 2022 Aug 2.
Quantifying species trophic interaction strengths is crucial for understanding community dynamics and has significant implications for pest management and species conservation. DNA-based methods to identify species interactions have revolutionized these efforts, but a significant limitation is the poor ability to quantify the strength of trophic interactions, that is the biomass or number of prey consumed. We present an improved pipeline, called Lazaro, to map unassembled shotgun reads to a comprehensive arthropod mitogenome database and show that the number of prey reads detected is quantitatively predicted from the prey biomass consumed, even for indirect predation. Two feeding bioassays were performed: starved coccinellid larvae consuming different numbers of aphids (Prey Quantity bioassay), and starved coccinellid larvae consuming a chrysopid larvae that had consumed aphids (Direct and Indirect Predation bioassay). Prey taxonomic assignment against a mitochondrial genome database had high accuracy (99.8% positive predictive value) and the number of prey reads was directly related to the number of prey consumed and inversely related to the elapsed time since consumption with high significance (r = .932, p = 4.92E-6). Aphids were detected up to 6 h after direct predation plus 3 h after indirect predation (9 h in total) and detection was related to the predator-specific decay rates. Lazaro enabled quantitative predictions of prey consumption across multiple trophic levels with high taxonomic resolution while eliminating all false positives, except for a few confirmed contaminants, and may be valuable for characterizing prey consumed by field-sampled predators. Moreover, Lazaro is readily applicable for species diversity determination from any degraded environmental DNA.
量化物种的营养相互作用强度对于理解群落动态至关重要，并且对害虫管理和物种保护具有重要意义。基于 DNA 的方法来识别物种相互作用已经彻底改变了这些努力，但一个显著的限制是量化营养相互作用强度（即消耗的猎物生物量或数量）的能力较差。我们提出了一种改进的管道，称为 Lazaro，它可以将未组装的霰弹枪读数映射到综合节肢动物线粒体基因组数据库，并表明即使是间接捕食，从消耗的猎物生物量也可以定量预测检测到的猎物读数的数量。进行了两项喂养生物测定：饥饿的瓢虫幼虫消耗不同数量的蚜虫（猎物数量生物测定），以及饥饿的瓢虫幼虫消耗已消耗蚜虫的草蛉幼虫（直接和间接捕食生物测定）。针对线粒体基因组数据库的猎物分类学分配具有很高的准确性（99.8%的阳性预测值），猎物读数的数量与消耗的猎物数量直接相关，与消耗后经过的时间成反比，具有高度显著性（r = .932，p = 4.92E-6）。在直接捕食后加上间接捕食后 3 小时（总共 9 小时）可以检测到蚜虫，并且检测结果与捕食者特定的衰减率有关。Lazaro 能够以高分类分辨率对多个营养水平的猎物消耗进行定量预测，同时消除了所有假阳性，除了少数确认的污染物外，并且可能对表征现场采样捕食者消耗的猎物具有重要价值。此外，Lazaro 很容易适用于从任何退化的环境 DNA 中确定物种多样性。
