Hollowell A C, Regus J U, Gano K A, Bantay R, Centeno D, Pham J, Lyu J Y, Moore D, Bernardo A, Lopez G, Patil A, Patel S, Lii Y, Sachs J L
Department of Biology, University of California, Riverside, CA, 92521, USA.
Institute for Integrative Genome Biology, University of California, Riverside, CA, 95616, USA.
Microb Ecol. 2016 Apr;71(3):700-10. doi: 10.1007/s00248-015-0685-5. Epub 2015 Oct 14.
The patterns and drivers of bacterial strain dominance remain poorly understood in natural populations. Here, we cultured 1292 Bradyrhizobium isolates from symbiotic root nodules and the soil root interface of the host plant Acmispon strigosus across a >840-km transect in California. To investigate epidemiology and the potential role of accessory loci as epidemic drivers, isolates were genotyped at two chromosomal loci and were assayed for presence or absence of accessory "symbiosis island" loci that encode capacity to form nodules on hosts. We found that Bradyrhizobium populations were very diverse but dominated by few haplotypes-with a single "epidemic" haplotype constituting nearly 30 % of collected isolates and spreading nearly statewide. In many Bradyrhizobium lineages, we inferred presence and absence of the symbiosis island suggesting recurrent evolutionary gain and or loss of symbiotic capacity. We did not find statistical phylogenetic evidence that the symbiosis island acquisition promotes strain dominance and both symbiotic and non-symbiotic strains exhibited population dominance and spatial spread. Our dataset reveals that a strikingly few Bradyrhizobium genotypes can rapidly spread to dominate a landscape and suggests that these epidemics are not driven by the acquisition of accessory loci as occurs in key human pathogens.
在自然种群中，细菌菌株优势的模式和驱动因素仍未得到充分了解。在这里，我们从加利福尼亚州一条超过840公里长的样带中，从宿主植物硬毛相思的共生根瘤和土壤根际界面培养了1292株慢生根瘤菌分离株。为了研究流行病学以及辅助基因座作为流行驱动因素的潜在作用，我们对分离株在两个染色体基因座进行了基因分型，并检测了编码在宿主上形成根瘤能力的辅助“共生岛”基因座的有无。我们发现慢生根瘤菌种群非常多样化，但由少数单倍型主导——一种单一的“流行”单倍型占收集到的分离株近30%，并几乎在全州范围内传播。在许多慢生根瘤菌谱系中，我们推断共生岛的有无表明共生能力反复出现进化获得和/或丧失。我们没有发现统计学上的系统发育证据表明共生岛的获得促进了菌株优势，共生和非共生菌株都表现出种群优势和空间传播。我们的数据集表明，极少数慢生根瘤菌基因型能够迅速传播以主导一个区域，并表明这些流行并非像关键人类病原体那样由辅助基因座的获得所驱动。
