Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater Genus Limnohabitans
Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater Genus Limnohabitans
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DOI：
10.1128/aem.00140-20
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发表时间：
2020-03
影响因子：
4.4
通讯作者：
R. Props;Vincent J. Denef
中科院分区：
文献类型：
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作者：
R. Props;Vincent J. Denef
Limnohabitans是全球淡水生态系统中重要的碳循环细菌分类类群。在这里，我们研究了不同的Limnohabitans谱系的基因组多样性。我们重点研究了该属的肢体谱系，该属分布于全球，通常丰富，其丰度显示出对环境变化的基本不变。我们的数据表明，肢体谱系实际上是由多个共存的种群组成的，这些种群的组成和基因组特征与温度和营养水平的变化有关。该谱系的基因表达谱表明趋化性和运动性在适应环境条件方面的重要性，这些特征尚未与Limnohabitans属相关。大多数淡水细菌群落的特征是少数优势分类群，这些分类群通常在全世界的淡水生物群系中普遍存在。我们对这些分类群的基因组多样性的了解仅限于分类群的一个子集。在这里，我们研究了Limnohabitans（一种将碳从初级生产者输送到更高营养水平的淡水属）的基因组多样性，以实现丰富和无处不在。我们重建了8个假定的Limnohabitans宏基因组组装基因组（MAGs），这些基因组来自位于密歇根湖（地球上最大的地表淡水系统的一部分）广泛环境梯度沿线的站点。新菌株推断分析共解析了23个菌株，这些菌株强烈划分为两个栖息地特定的聚类，并同时发生来自不同谱系的菌株。最大数量的菌株属于丰富的肢体谱系，这是以前没有实现的可靠的原位菌株描绘。我们的数据表明，温度和营养水平可能是与Limnohabitans属微多样化相关的重要环境参数。此外，在低磷和高磷条件下占优势的菌株比在不同温度下丰富的菌株具有更大的基因组分化。比较基因组学和基因表达分析证明了肢体群体表现出细胞运动性和趋化性的能力，这是一种尚未与Limnohabitans分离株相关的表型。我们的发现拓宽了基于历史标记基因的Limnohabitans微多样性调查，并提供了基因组多样性及其在淡水梯度中的功能意义的原位证据。Limnohabitans是全球淡水生态系统中重要的碳循环细菌分类类群。在这里，我们研究了不同的Limnohabitans谱系的基因组多样性。我们重点研究了该属的肢体谱系，该属分布于全球，通常丰富，其丰度显示出对环境变化的基本不变。我们的数据表明，肢体谱系实际上是由多个共存的种群组成的，这些种群的组成和基因组特征与温度和营养水平的变化有关。该谱系的基因表达谱表明趋化性和运动性在适应环境条件方面的重要性，这些特征尚未与Limnohabitans属相关。
Limnohabitans is an important bacterial taxonomic group for cycling carbon in freshwater ecosystems worldwide. Here, we examined the genomic diversity of different Limnohabitans lineages. We focused on the LimB lineage of this genus, which is globally distributed and often abundant, and its abundance has shown to be largely invariant to environmental change. Our data show that the LimB lineage is actually comprised of multiple cooccurring populations for which the composition and genomic characteristics are associated with variations in temperature and nutrient levels. The gene expression profiles of this lineage suggest the importance of chemotaxis and motility, traits that had not yet been associated with the Limnohabitans genus, in adapting to environmental conditions. ABSTRACT Most freshwater bacterial communities are characterized by a few dominant taxa that are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic diversity within these taxonomic groups is limited to a subset of taxa. Here, we investigated the genomic diversity that enables Limnohabitans, a freshwater genus key in funneling carbon from primary producers to higher trophic levels, to achieve abundance and ubiquity. We reconstructed eight putative Limnohabitans metagenome-assembled genomes (MAGs) from stations located along broad environmental gradients existing in Lake Michigan, part of Earth’s largest surface freshwater system. De novo strain inference analysis resolved a total of 23 strains from these MAGs, which strongly partitioned into two habitat-specific clusters with cooccurring strains from different lineages. The largest number of strains belonged to the abundant LimB lineage, for which robust in situ strain delineation had not previously been achieved. Our data show that temperature and nutrient levels may be important environmental parameters associated with microdiversification within the Limnohabitans genus. In addition, strains predominant in low- and high-phosphorus conditions had larger genomic divergence than strains abundant under different temperatures. Comparative genomics and gene expression analysis yielded evidence for the ability of LimB populations to exhibit cellular motility and chemotaxis, a phenotype not yet associated with available Limnohabitans isolates. Our findings broaden historical marker gene-based surveys of Limnohabitans microdiversification and provide in situ evidence of genome diversity and its functional implications across freshwater gradients. IMPORTANCE Limnohabitans is an important bacterial taxonomic group for cycling carbon in freshwater ecosystems worldwide. Here, we examined the genomic diversity of different Limnohabitans lineages. We focused on the LimB lineage of this genus, which is globally distributed and often abundant, and its abundance has shown to be largely invariant to environmental change. Our data show that the LimB lineage is actually comprised of multiple cooccurring populations for which the composition and genomic characteristics are associated with variations in temperature and nutrient levels. The gene expression profiles of this lineage suggest the importance of chemotaxis and motility, traits that had not yet been associated with the Limnohabitans genus, in adapting to environmental conditions.