Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
Department of Fish, Wildlife and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA.
Appl Environ Microbiol. 2021 Mar 11;87(7). doi: 10.1128/AEM.02635-20.
Metal contamination from mining or natural weathering is a common feature of surface waters in the American west. Advances in microbial analyses have created the potential for routine sampling of aquatic microbiomes as a tool to assess the quality of stream habitat. We sought to determine if microbiome diversity and membership were affected by metal contamination and identify candidate microbial taxa to be used to indicate metal stress in stream ecosystems. We evaluated microbiome membership from sediments at multiple sites within the principal drainage of an EPA superfund site near the headwaters of the Upper Arkansas River, Leadville, CO. From each sample, we extracted DNA and sequenced the 16S rRNA gene amplicon on the Illumina MiSeq platform. We used the remaining sediments to simultaneously evaluate environmental metal concentrations. We also conducted an artificial stream mesocosm experiment using sediments collected from two of the observational study sites. The mesocosm experiment had a two-by-two factorial design: (i) location (upstream or downstream of contaminating tributary), and (ii) treatment (metal exposure or control). We found no difference in diversity between upstream and downstream sites in the field. Similarly, diversity changed very little following experimental metal exposure. However, microbiome membership differed between upstream and downstream locations and experimental metal exposure changed microbiome membership in a manner that depended on origin of the sediments used in each mesocosm. Our results suggest that microbiomes can be reliable indicators of ecosystem metal stress even when surface water chemistry and other metrics used to assess ecosystem health do not indicate ecosystem stress. Results presented in this study, in combination with previously published work on this same ecosystem, are consistent with the idea that a microbial response to metals at the base of the food web may be affecting primary consumers. If effects of metals are mediated through shifts in the microbiome, then microbial metrics, as presented here, may aid in the assessment of stream ecosystem health, which currently does not include assessments of the microbiome.
采矿或自然风化造成的金属污染是美国西部地表水的一个常见特征。微生物分析的进步为常规采集水生微生物组作为评估溪流生境质量的工具创造了条件。我们试图确定微生物组的多样性和成员是否受到金属污染的影响，并确定候选微生物类群，以用于指示溪流生态系统中的金属胁迫。我们评估了科罗拉多州莱德维尔市上游阿肯色河源头附近一个 EPA 超级基金场地主要排水系统内多个地点沉积物中的微生物组成员。从每个样本中，我们提取 DNA 并在 Illumina MiSeq 平台上对 16S rRNA 基因扩增子进行测序。我们还使用剩余的沉积物同时评估环境金属浓度。我们还使用从两个观测研究地点收集的沉积物进行了人工溪流中观实验。该中观实验采用了二因素二水平的设计：（i）地点（受污染支流的上游或下游）和（ii）处理（金属暴露或对照）。我们在野外没有发现上游和下游地点之间多样性的差异。同样，实验性金属暴露后多样性变化很小。然而，微生物组成员在上下游位置和实验性金属暴露之间存在差异，微生物组成员的变化方式取决于每个中观系统中使用的沉积物的来源。我们的结果表明，即使地表水化学和其他用于评估生态系统健康的指标没有指示生态系统胁迫，微生物组也可以成为生态系统金属胁迫的可靠指标。本研究中提出的结果与同一生态系统的先前研究结果一致，表明金属在食物网底部对微生物的影响可能正在影响初级消费者。如果金属的影响是通过微生物组的变化介导的，那么这里提出的微生物指标可能有助于评估溪流生态系统的健康状况，而目前的评估不包括对微生物组的评估。
