Environmental Controls Over Actinobacteria Communities in Ecological Sensitive Yanshan Mountains Zone

Abstract

The Yanshan Mountains are one of the oldest mountain ranges in the world. They are located in an ecologically sensitive zone in northern China near the Hu Huanyong Line. In this metagenomic study, we investigated the diversity of Actinobacteria in soils at 10 sites (YS1–YS10) on the Yanshan Mountains. First, we assessed the effect of different soil prtreatment on Actinobacteria recovery. With the soil pretreatment method: air drying of the soil sample, followed by exposure to 120°C for 1 h, we observed the higher Actinobacteria diversity in a relatively small number of clone libraries. No significant differences were observed in the Actinobacterial diversity of soils from sites YS2, YS3, YS4, YS6, YS8, YS9, or YS10 (P > 0.1). However, there were differences (P < 0.05) from the YS7 site and other sites, especially in response to environmental change. And we observed highly significant differences (P < 0.001) in Actinobacterial diversity of the soil from YS7 and that from YS4 and YS8 sites. The climatic characteristics of mean active accumulated temperature, annual mean precipitation, and annual mean temperature, and biogeochemical data of total phosphorus contributed to the diversity of Actinobacterial communities in soils at YS1, YS3, YS4, and YS5 sites. Compared to the climatic factors, the biogeochemical factors mostly contributed in shaping the Actinobacterial community. This work provides evidence that the diversity of Actinobacterial communities in soils from the Yashan Mountains show regional biogeographic patterns and that community membership change along the north-south distribution of the Hu Huanyong Line.

Seasonal dynamics of lotic bacterial communities assessed by 16S rRNA gene amplicon deep sequencing

“…Though, Actinobacteria demonstrated a remarkably positive correlation with Ptot ( Fig. 5), which could very well be linked to their active involvement in phosphate solubilization 30,31 . Notably, the major seasonal dynamic of bacterial assemblage was driven, significantly, by TSS ( Fig.…”

Microbiology Meets Archaeology: Soil Microbial Communities Reveal Different Human Activities at Archaic Monte Iato (Sixth Century BC)

“…This bacterial group exhibits a wide range of morphologies, lifestyles, and physiological and metabolic properties; members of some orders are spore-formers and thus able to withstand unfavorable conditions [45]. They are widely distributed in soil ecosystems, where they play a crucial role in the recycling of biomaterials by decomposition and humus formation [46].…”

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

“…Given the rapid and ongoing progress in sequencing technologies (Mavromatis et al, 2012 ), classifications based on whole genome sequences and associated bioinformatic tools are addressing these needs as they are based on millions of unit characters and thereby provide a step change in reliability, as evidenced by significantly high average bootstrap support in phylogenomic trees (Breider et al, 2014 ; Meier-Kolthoff et al, 2014a ). In contrast, trees based on a few thousand nucleotides (Tang et al, 2016 ) tend to have branches with low bootstrap values; the same limitation applies, albeit to a lesser extent, to multi-locus sequence analyses of conserved housekeeping genes (Glaeser and Kämpfer, 2015 ), which can hardly be called genome-scale (Klenk and Göker, 2010 ). Phylogenomic methods have already been applied to elucidate the classification of complex actinobacterial taxa, such as the genera Amycolatopsis, Micromonospora, Rhodococcus , and Salinispora (Sangal et al, 2016 ; Tang et al, 2016 ; Jensen, 2017 ; Carro et al, 2018 ), and in some cases has led to marked reclassification (Montero-Calasanz et al, 2017 ).…”

“…In contrast, trees based on a few thousand nucleotides (Tang et al, 2016 ) tend to have branches with low bootstrap values; the same limitation applies, albeit to a lesser extent, to multi-locus sequence analyses of conserved housekeeping genes (Glaeser and Kämpfer, 2015 ), which can hardly be called genome-scale (Klenk and Göker, 2010 ). Phylogenomic methods have already been applied to elucidate the classification of complex actinobacterial taxa, such as the genera Amycolatopsis, Micromonospora, Rhodococcus , and Salinispora (Sangal et al, 2016 ; Tang et al, 2016 ; Jensen, 2017 ; Carro et al, 2018 ), and in some cases has led to marked reclassification (Montero-Calasanz et al, 2017 ). However, a comprehensive analysis of the phylum Actinobacteria based on truly genome-scale methods has not been undertaken.…”