Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg Universitygrid.5117.2, Aalborg, Denmark.
Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
mSystems. 2022 Jun 28;7(3):e0001622. doi: 10.1128/msystems.00016-22. Epub 2022 Apr 25.
" Accumulibacter" was the first microorganism identified as a polyphosphate-accumulating organism (PAO) important for phosphorus removal from wastewater. Members of this genus are diverse, and the current phylogeny and taxonomic framework appear complicated, with most publicly available genomes classified as " Accumulibacter phosphatis," despite notable phylogenetic divergence. The marker gene allows for a finer-scale differentiation into different "types" and "clades"; nevertheless, taxonomic assignments remain inconsistent across studies. Therefore, a comprehensive reevaluation is needed to establish a common understanding of this genus, in terms of both naming and basic conserved physiological traits. Here, we provide this reassessment using a comparison of genome, , and 16S rRNA gene-based approaches from comprehensive data sets. We identified 15 novel species, along with " Accumulibacter phosphatis," " Accumulibacter delftensis," and " Accumulibacter aalborgensis." To compare the species , we designed new species-specific fluorescence hybridization (FISH) probes and revealed their morphology and arrangement in activated sludge. Based on the MiDAS global survey, ". Accumulibacter" species were widespread in wastewater treatment plants (WWTPs) with phosphorus removal, indicating process design as a major driver for their abundance. Genome mining for PAO-related pathways and FISH-Raman microspectroscopy confirmed the potential for PAO metabolism in all ". Accumulibacter" species, with detection of the typical PAO storage polymers. Genome annotation further revealed differences in the nitrate/nitrite reduction pathways. This provides insights into the niche differentiation of these lineages, potentially explaining their coexistence in the same ecosystem while contributing to overall phosphorus and nitrogen removal. " Accumulibacter" is the most studied PAO, with a primary role in biological nutrient removal. However, the species-level taxonomy of this lineage is convoluted due to the use of different phylogenetic markers or genome sequencing approaches. Here, we redefined the phylogeny of these organisms, proposing a comprehensive approach which could be used to address the classification of other diverse and uncultivated lineages. Using genome-resolved phylogeny, compared to phylogeny based on the 16S rRNA gene and other phylogenetic markers, we obtained a higher-resolution taxonomy and established a common understanding of this genus. Furthermore, genome mining of genes and pathways of interest, validated by application of a new set of FISH probes and Raman microspectroscopy, provided additional high-resolution metabolic insights into these organisms.
"Accumulibacter" 是最早被鉴定为具有从废水中去除磷能力的聚磷酸盐积累菌（PAO）的微生物之一。该属成员具有多样性，目前的系统发育和分类框架似乎很复杂，大多数公开的基因组被归类为“Accumulibacter phosphatis”，尽管存在明显的系统发育分歧。标记基因允许更精细地细分为不同的“类型”和“分支”；然而，在不同的研究中，分类仍然不一致。因此，需要进行全面的重新评估，以建立对该属的共同理解，包括命名和基本保守的生理特征。在这里，我们使用来自综合数据集的基因组、 和 16S rRNA 基因方法的比较提供了这种重新评估。我们鉴定了 15 个新物种，以及“Accumulibacter phosphatis”、“Accumulibacter delftensis”和“Accumulibacter aalborgensis”。为了比较这些物种，我们设计了新的种特异性荧光杂交（FISH）探针，并揭示了它们在活性污泥中的形态和排列。基于 MiDAS 全球调查，“Accumulibacter”物种广泛存在于具有除磷能力的污水处理厂（WWTP）中，表明工艺设计是其丰度的主要驱动因素。对与 PAO 相关途径的基因组挖掘和 FISH-Raman 微光谱学证实了所有“Accumulibacter”物种中都存在 PAO 代谢的潜力，并检测到典型的 PAO 储存聚合物。基因组注释进一步揭示了硝酸盐/亚硝酸盐还原途径的差异。这为这些谱系的生态位分化提供了深入的了解，这可能解释了它们在同一生态系统中共存的原因，同时有助于磷和氮的去除。“Accumulibacter”是研究最多的 PAO，在生物营养去除中起主要作用。然而，由于使用了不同的系统发育标记或基因组测序方法，该谱系的种级分类仍然很复杂。在这里，我们重新定义了这些生物体的系统发育，提出了一种综合方法，可以用于解决其他具有多样性和未培养谱系的分类问题。使用基于基因组分辨率的系统发育与基于 16S rRNA 基因和其他系统发育标记的系统发育进行比较，我们获得了更高分辨率的分类，并对该属建立了共同的理解。此外，通过应用一组新的 FISH 探针和 Raman 微光谱学对感兴趣的基因和途径进行基因组挖掘，为这些生物体提供了更多的高分辨率代谢见解。
