A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils

Abstract

An integrated view of bacterial and archaeal diversity in saline soil habitats is essential for understanding the biological and ecological processes and exploiting potential of microbial resources from such environments. This study examined the collective bacterial and archaeal diversity in saline soils using a meta-analysis approach. All available 16S rDNA sequences recovered from saline soils were retrieved from publicly available databases and subjected to phylogenetic and statistical analyses. A total of 9,043 bacterial and 1,039 archaeal sequences, each longer than 250 bp, were examined. The bacterial sequences were assigned into 5,784 operational taxonomic units (OTUs, based on C97 % sequence identity), representing 24 known bacterial phyla, with Proteobacteria (44.9 %), Actinobacteria (12.3 %), Firmicutes (10.4 %), Acidobacteria (9.0 %), Bacteroidetes (6.8 %), and Chloroflexi (5.9 %) being predominant. Lysobacter (12.8 %) was the dominant bacterial genus in saline soils, followed by Sphingomonas (4.5 %), Halomonas (2.5 %), and Gemmatimonas (2.5 %). Archaeal sequences were assigned to 602 OTUs, primarily from the phyla Euryarchaeota (88.7 %) and Crenarchaeota (11.3 %).Halorubrum and Thermofilum were the dominant archaeal genera in saline soils. Rarefaction analysis indicated that less than 25 % of bacterial diversity, and approximately 50 % of archaeal diversity, in saline soil habitats has been sampled. This analysis of the global bacterial and archaeal diversity in saline soil habitats can guide future studies to further examine the microbial diversity of saline soils.

Salinity and Bacterial Diversity: To What Extent Does the Concentration of Salt Affect the Bacterial Community in a Saline Soil?

“…Some of the bacterial phyla found in the salt-affected soil under examination were also reported by Ma and Gong [12]. Using meta-analysis, these authors retrieved 10,082 sequences longer than 250 bp from the two databases GenBank and RDP, using the search terms “saline” OR “hyper saline”, AND “soil” AND “16S”.…”

Shifts in soil microbial metabolic activities and community structures along a salinity gradient of irrigation water in a typical arid region of China

“…The dominant groups in all saline water irrigated soils were Planctomycetes, Bacteroidetes and Proteobacteria, followed by Actinobacteria, Chloroflexi, Gemmatimonadetes and Acidobacteria. Some of the above bacterial phyla were similarly found in the saltaffected soils (Ma and Gong, 2013), which were reported that 90% of the bacterial sequences were belonged to six phyla (Proteobacteria, Actinobacteria, Firmicutes, Acidobacteria, Bacteroidetes and Chloroflexi). We noticed that the relative abundance of Proteobacteria increased significantly with irrigation salinity.…”

A Meta-Analysis of the Bacterial and Archaeal Diversity Observed in Wetland Soils

“…The distance cut-off for other taxonomic ranks was set as follows: 0.05, genus; 0.10, family; 0.15, class/order; and 0.2, phylum. All the estimated asymptotes of the rarefaction curve were determined through R package monomol (https://github.com/binma/monomol) [40]. The coverage percentages were calculated as described by Nelson et al [41].…”