Reliable identification and quantification of bioaerosols is fundamental in aerosol microbiome research, highlighting the importance of using sampling equipment with well-defined performance characteristics. Following advances in sequencing technology, shotgun metagenomic sequencing (SMS) of environmental samples is now possible. However, SMS of air samples is challenging due to low biomass, but with the use of high-volume air samplers sufficient DNA yields can be obtained. Here we investigate the sampling performance and comparability of two hand-portable, battery-operated, high-volume electret filter air samplers, SASS 3100 and ACD-200 Bobcat, previously used in SMS-based aerosol microbiome research. SASS and Bobcat consistently delivered end-to-end sampling efficiencies > 80% during the aerosol chamber evaluation, demonstrating both as effective high-volume air samplers capable of retaining quantitative associations. Filter recovery efficiencies were investigated with manual and sampler-specific semi-automated extraction procedures. Bobcat semi-automated extraction showed reduced efficiency compared to manual extraction. Bobcat tended towards higher sampling efficiencies compared to SASS when combined with manual extraction. To evaluate real-world sampling performance, side-by-side SASS and Bobcat sampling was done in a semi-suburban outdoor environment and subway stations. SMS-based microbiome profiles revealed that highly abundant bacterial species had similar representation across samplers. While alpha diversity did not vary for the two samplers, beta diversity analyses showed significant within-pair variation in subway samples. Certain species were found to be captured only by one of the two samplers, particularly in subway samples. SASS and Bobcat were both found capable of collecting sufficient aerosol biomass amounts for SMS, even at sampling times down to 30 min. Bobcat semi-automated filter extraction was shown to be less effective than manual filter extraction. For the most abundant species the samplers were comparable, but systematic sampler-specific differences were observed at species level. This suggests that studies conducted with these highly similar air samplers can be compared in a meaningful way, but it would not be recommended to combine samples from the two samplers in joint analyses. The outcome of this work contributes to improved selection of sampling equipment for use in SMS-based aerosol microbiome research and highlights the importance of acknowledging bias introduced by sampling equipment and sample recovery procedures.

中文翻译：

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大容量驻极体过滤器空气采样器在气溶胶微生物组研究中的性能评估

可靠地鉴定和定量生物气溶胶是气溶胶微生物组研究的基础，突显了使用具有明确性能特征的采样设备的重要性。随着测序技术的进步，环境样品的shot弹枪宏基因组测序（SMS）现在成为可能。但是，由于生物量低，空气样品的SMS极具挑战性，但是使用高容量的空气采样器可以获得足够的DNA产量。在这里，我们调查了以前用于基于SMS的气溶胶微生物组研究的两个便携式，电池供电的大容量驻极体过滤空气采样器SASS 3100和ACD-200山猫的采样性能和可比性。在气雾室评估期间，SASS和山猫始终提供大于80％的端到端采样效率，展示了这两种有效的高容量空气采样器，能够保留定量关联。使用手动和特定于采样器的半自动提取程序研究了过滤器的回收效率。与手动提取相比，山猫半自动提取显示出降低的效率。当与手动提取结合使用时，与SASS相比，山猫倾向于更高的采样效率。为了评估现实世界的采样性能，在半郊区室外环境和地铁站中进行了并排SASS和山猫采样。基于SMS的微生物组概况显示，高度丰富的细菌物种在采样器中具有相似的表示。尽管两个采样器的alpha多样性没有变化，但beta多样性分析显示地铁样本中的配对对内存在显着变化。发现某些物种仅被两个采样器之一捕获，特别是在地铁采样中。SASS和山猫都被发现能够收集足够的气溶胶生物量用于SMS，即使采样时间长达30分钟也是如此。山猫半自动过滤器萃取比手动过滤器萃取效果差。对于最丰富的物种，采样器具有可比性，但是在物种级别观察到系统的采样器特定差异。这表明可以用有意义的方式对使用这些高度相似的空气采样器进行的研究进行比较，但是不建议在联合分析中将两个采样器的采样合并在一起。