Diversity of Bacteria and the Characteristics of Actinobacteria Community Structure in Badain Jaran Desert and Tengger Desert of China

Abstract

To assess the diversity of actinobacterial taxa in desert sands and obtain the novel microbial resources, 79 and 50 samples were collected from the Badain Jaran (BJD) and Tengger Deserts (TGD) of China, respectively. High-throughput sequencing (HTS) of environmental 16S rRNA genes within these samples was conducted on an Illumina Miseq platform, using universal bacterial primers targeting the V3–V4 hypervariable region. Based on the HTS analyses, cultivation-dependent (CULD) techniques were optimized to identify the cultivable Actinobacteria members. A total of 346,766 16S rRNA gene reads comprising 3,365 operational taxonomic units (OTUs) were obtained from the BJD sands using HTS, while 170,583 reads comprising 1,250 OTUs were detected in the TGD sands. Taxonomic classification indicated that Actinobacteria was the predominant phylum, comprising 35.0 and 29.4% of the communities in BJD and TGD sands, respectively. Among the Actinobacteria, members of the Geodermatophilaceae were considerably abundant in both deserts, indicating that they represent ubiquitous populations within the deserts. At the genus level, Arthrobacter spp. and Kocuria spp. were dominant, and corresponded to 21.2 and 5.3% of the actinobacterial communities in BJD and TGD deserts, respectively. A total of 786 and 376 actinobacterial strains were isolated and identified from BJD and TGD samples, respectively. The isolates comprised 73 genera of 30 families within the phylum Actinobacteria. In addition to the Geodermatophilaceae, Streptomyces spp. were a prominent component of the isolates, comprising 25% of the isolates from BJD and 17.5% of those from TGD. Comparison of the actinobacterial community structure in other ecosystems indicated that Geodermatophilaceae was the main actinobacterial group in desert sands, which is consistent with our results. Additionally, in these desert habits, Geodermatophilaceae and some other core groups may promote or inhabit the subsequent members' occurrence or prosper to shape the bacteria community structure. However, it should be noted that a number of other low-abundance bacteria appear to be specific to desert sands, which are worth further investigation. In antimicrobial activity assays, 10.36 % of the tested isolates showed antimicrobial activities in one or more screens. Importantly, 37 of the newly isolated strains reported here represent novel taxa that could be valuable resources for further research of novel secondary metabolites and their ecological significance in deserts.

Diverse Bacterial Communities From Qaidam Basin of the Qinghai–Tibet Plateau: Insights Into Variations in Bacterial Diversity Across Different Regions

“…In contrast to our study, Takahashi et al (1996), Okoro et al (2009), and Ding et al (2012) reported highly diverse bacterial communities in desert habitats. In addition, Geodermatophilaceae was only found in the E0 samples (surface soil in the east region) in our study, but it has been reported in the Heihe River Basin of Northwest China (Zhang et al, 2019) and was found to be dominant in both the Tengger and the Badain Jaran deserts in China (Sun et al, 2018). Furthermore, Hydrogenophaga was detected in our study, but not in other studies of deserts.…”

Elucidating the ecological networks in stone‐dwelling microbiomes

“…Actinobacteria extend their hyphae growth to promote community stone attachment, Cyanobacteria support the community through photosynthesis, and Proteobacteria aid in the biofilm development (Saiz‐Jimenez et al ., ; Ortega‐Morales et al ., ; Kemmling et al ., ; Kiel and Gaylarde, ; Abdulla, ; Cockell et al ., ). In addition, many of these organisms, particularly Actinobacteria and Cyanobacteria, are tolerant to heavy metals found in the stones, produce pigments to protect from UV light and can survive with minimal nutrient access on stone surfaces (Potts and Friedmann, ; Eppard et al ., ; Scheerer et al ., 2001; Sun et al ., ). These three phyla were more specifically represented in the two‐way cluster analysis and metagenomic bins, which included Rubrobacter , Geodermatophilaceae, Nostocaceae, Chroococcidiospaceae and Sphingomonas .…”

“…In addition, many of these organisms, particularly Actinobacteria and Cyanobacteria, are tolerant to heavy metals found in the stones, produce pigments to protect from UV light and can survive with minimal nutrient access on stone surfaces (Potts and Friedmann, 1981;Eppard et al, 1996;Scheerer et al, 2001;Sun et al, 2018). These three phyla were more specifically represented in the twoway cluster analysis and metagenomic bins, which included Rubrobacter, Geodermatophilaceae, Nostocaceae, Chroococcidiospaceae and Sphingomonas.…”

Epiphytic and Endophytic Bacteria on Olive Tree Phyllosphere: Exploring Tissue and Cultivar Effect

“…Members of detected phyla, in particular of Actinobacteria and Firmicutes, often prevail in arid environments [46][47][48] due to their ability to resist to UV-radiation and desiccation [49]. Their resistance has been mostly attributed to their ability to produce photoprotective pigments [50] and to repair UVdamages through multiple mechanisms [51].…”