Stable Function, Dynamic Phylotypes: Microdiversity as a Reservoir for Resilience in Dehalococcoides

Organohalide-respiring bacteria (OHRB) are key contributors to global halogen cycling and mitigation of anthropogenic halogenated pollutants, yet their persistence is challenged by slow growth and restricted metabolic capacity. The mechanisms supporting long-term functional stability remain unclear. As a key OHRB, Dehalococcoides faces similar constraints, including declining abundance and loss or divergence of functional genes in bioaugmentation. Here we demonstrate that strain-level microdiversity within Dehalococcoides supports the resilience of community-scale dehalogenation. In AEDhc, a reconstructed consortium derived from eight Dehalococcoides-containing enrichment cultures, sequencing of a Dehalococcoides-specific marker gene revealed 30 distinct Dehalococcoides phylotypes coexisting within the community. Despite fluctuations in phylotype abundance over successive transfers, AEDhc consistently debrominated tetra- and pentabrominated diphenyl ethers (0.39 ± 0.06 - 0.45 ± 0.05 μM Br–/d), producing no detectable accumulation of intermediates. Proteomics analyses revealed that among 71 putative reductive dehalogenase (RDase) genes identified in metagenomic analysis, expression was consistently dominated by PcbA1-like and TceA-like RDases across transfers. These findings demonstrated that Dehalococcoides phylotypes can coexist and fluctuate dynamically even under constant cultivation conditions, with genetic variation serving as a reservoir of metabolic potential. Such microdiversity enhances functional stability and ecological resilience, highlighting the need to consider strain-level heterogeneity in bioremediation strategies.

有机卤呼吸细菌（Organohalide-respiring bacteria, OHRB）是全球卤族元素循环以及人为源卤化污染物消减的关键功能类群，但其存续常面临生长缓慢、代谢能力受限的挑战，维持其长期功能稳定性的内在机制仍未明确。作为一类关键的有机卤呼吸细菌，脱卤球菌属（Dehalococcoides）也面临类似限制：在生物强化过程中其丰度会下降，功能基因出现丢失或分化。本研究证实，脱卤球菌属内的菌株水平微多样性可提升群落规模脱卤作用的恢复力。在由8株含脱卤球菌属富集培养物重构的合成群落AEDhc中，通过对脱卤球菌属特异性标记基因的测序，发现群落内共存30种不同的脱卤球菌属系统型。尽管在连续传代过程中各系统型的丰度存在波动，但AEDhc始终能够对四溴联苯醚和五溴联苯醚进行脱溴反应（脱溴速率为0.39 ± 0.06 ~ 0.45 ± 0.05 μM Br–/d），且未检测到中间产物的积累。蛋白质组学分析显示，在宏基因组分析鉴定出的71个推定还原脱卤酶（reductive dehalogenase, RDase）基因中，各传代批次的基因表达始终以PcbA1样和TceA样还原脱卤酶为主。上述研究结果表明，即使在恒定的培养条件下，脱卤球菌属的不同系统型仍可共存并发生动态丰度波动，而遗传变异可作为代谢潜能的储备库。这类微多样性可提升群落的功能稳定性与生态恢复力，这凸显了在生物修复策略中需考虑菌株水平异质性的必要性。