Microbial Diversity in an Arid, Naturally Saline Environment

Bachran, Madlen; Kluge, Sindy; López-Fernández, Margarita; Cherkouk, Andrea

doi:10.1007/s00248-018-1301-2

Cited by 38 publications

(23 citation statements)

References 51 publications

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“…Based on cultured dependent approach, only some isolates affiliated to Haloferax , Halorubrum , Halorcula , Halogeometricum , and uncultured haloarchaeal strains have been successfully isolated from all samples which may due to the still unknown growth requirements of the species [ 121 ]. The discrepancy between the haloarchaeal diversity analysis achieved by all approaches are in accordance with those reported by other authors [ 43 , 122 ].…”

Section: Haloarchaeal Community Structure Between Sites Based On All Approachessupporting

confidence: 91%

Assessment of 16S rRNA Gene-Based Phylogenetic Diversity of Archaeal Communities in Halite-Crystal Salts Processed from Natural Saharan Saline Systems of Southern Tunisia

Najjari

Stathopoulou

Elmnasri³

et al. 2021

Biology

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A thorough assessment of the phylogenetic diversity and community structure of halophilic archaea from three halite-crystal salts, processed from two separated saline systems of Southern Tunisia has been performed using culture dependent and independent methods targeting different regions of 16S rRNA gene sequences including DGGE, 16S rRNA clone libraries and Illumina Miseq sequencing. Two samples, CDR (red halite-crystal salts) and CDW (white halite-crystal salts), were collected from Chott-Eljerid and one sample CDZ (white halite-crystal salts) from Chott Douz. Fourteen isolates were identified as Halorubrum, Haloferax, Haloarcula, and Halogeometricum genera members. Culture-independent approach revealed a high diversity of archaeal members present in all samples, represented by the Euryarchaeal phylum and the dominance of the Halobacteria class. Nanohaloarchaea were also identified only in white halite samples based on metagenomic analysis. In fact, a total of 61 genera were identified with members of the Halorhabdus, Halonotius, Halorubrum, Haloarcula, and unclassified. Halobacteriaceae were shared among all samples. Unexpected diversity profiles between samples was observed where the red halite crust sample was considered as the most diverse one. The highest diversity was observed with Miseq approach, nevertheless, some genera were detected only with 16S rRNA clone libraries and cultured approaches.

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Section: Haloarchaeal Community Structure Between Sites Based On All Approachessupporting

confidence: 91%

Assessment of 16S rRNA Gene-Based Phylogenetic Diversity of Archaeal Communities in Halite-Crystal Salts Processed from Natural Saharan Saline Systems of Southern Tunisia

Najjari

Stathopoulou

Elmnasri³

et al. 2021

Biology

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“…This trend is in agreement with the one reported by Wei et al (2020) for Chinese soils under monsoon climate. Archaea are abundantly found in desert saline soils, and their diversity is usually dominated by the orders Halobacteriales, Haloferacales, and Natrialbales (Bachran et al 2019). In our irrigated samples, Nitrososphaerales was the dominant order of archaea at low salinity, whereas Nitrososphaerales and Halobacteriales were equally dominant at high salinity.…”

Section: Soil Salinity As a Driver Of Microbial Diversitymentioning

confidence: 69%

“…In our irrigated samples, Nitrososphaerales was the dominant order of archaea at low salinity, whereas Nitrososphaerales and Halobacteriales were equally dominant at high salinity. We recall here that usually Archaea are unculturable microbes and many sequences cannot be assigned to a specific OTU, partially due to the limited resolution of V4 region of 16S rRNA gene for taxonomic assignment of Archaea (Bachran et al 2019).…”

Section: Soil Salinity As a Driver Of Microbial Diversitymentioning

confidence: 99%

Impact of a Nature-Inspired Engineered Soil Structure on Microbial Diversity and Community Composition in the Bulk Soil and Rhizosphere of Tomato Grown Under Saline Irrigation Water

Al-Ismaily

Al‐Mayahi

Al-Siyabi

et al. 2020

J Soil Sci Plant Nutr

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Smart Capillary Barrier (SCB) has been recently promoted to decrease soil salinity and improve water use efficiency and the sustainability of arid land agriculture. In this study, we investigated the effect of SCB on soil microbial diversity, enumeration, and respiration in a tomato field trial. SCB soil and control (unstructured homogenous soils, H) plots were irrigated with four levels of salinity (EC w = 0.8, 3, 6, and 9 dS m −1). Microbial diversity was assessed by ITS and 16S rRNA gene sequencing, enumeration of culturable heterotrophs by agar plates, and microbial respiration by MicroResp™ assays. Salinity was the main driver of the soil microbial diversity, showing a substantial reduction in the number of operational taxonomic units (− 8% for both bacteria and fungi), enumeration of culturable heterotrophs (− 51% for bacteria and − 53% for fungi), and respiration (− 18%) at 9 dS m −1 water salinity. Microbial community composition was significantly different between the SCB and H soils, as evidenced by multivariate analyses and by the appearance of 3352 unique operational taxonomic units at SCB samples that were absent in H plots. The SCB soil showed a steeper metabolic quotient increase in response to soil salinity than the H soils. The abundance of functional microbes such as nitrogen-fixing and nitrifying prokaryotes, as well as mycorrhiza, was also significantly increased in the SCB soils in comparison with the H soils. Our findings suggest that adopting SCB design leads to higher overall soil microbial biodiversity, including those communities unable to withstand extreme soil salinity conditions.

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“…Several previous studies have also shown a strong influence of water availability on bacterial community variations, with bacterial dissimilarity being generally higher with increasing precipitation distance on dryland (Nielsen and Ball, 2015; Wang et al, 2015). Furthermore, in arid land, the pressure of water availability is often accompanied by increased salinity content owing to rapid evaporation, leading to the accumulation of salinity (Bachran et al, 2018; Zhao et al, 2019). In this regard, some studies have reported that salinity exerts a strong selection pressure on the microbial community, resulting in deterministic processes in microbial assembly (Rath et al, 2019; Zhang K. et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Soil Property and Plant Diversity Determine Bacterial Turnover and Network Interactions in a Typical Arid Inland River Basin, Northwest China

Wang

et al. 2019

Front. Microbiol.

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Water sources from the lower reaches of the Heihe River northwest China, located in an arid area impacted by environmental stresses, have promoted changes to the local soil and plant conditions; however, our understanding of variations and drivers of soil bacterial communities in an arid inland river basin remains unclear. Therefore, we collected 39 soil samples from a riparian oasis zone (ROZ) to the circumjacent desert zone (CDZ) at the lower reaches of Heihe River to evaluate bacterial communities based on the 16S rRNA gene data. We found that the bacterial community composition differed between ROZ and CDZ habitats, with significantly higher relative abundance of the phyla Gemmatimonadetes and Acidobacteria in ROZ, whereas the abundance of the phyla Actinobacteria and Deinococcus–Thermus was greater in CDZ. The difference in the bacterial community was almost entirely generated by the species turnover rather than the nestedness among all samples. In addition, we found that bacterial α-diversity index showed no significant difference between ROZ and CDZ habitats. The distance-decay analysis showed that spatial distance, plant community, soil property, and plant functional trait were correlated with bacterial community variations. However, the variation partition analysis (VPA) revealed that both soil properties and plant community strongly explained the difference [such as soil water content (WC), soil silt content, and plant community structure] compared with plant functional traits in bacterial β-diversity and species turnover. Based on a co-occurrence network analysis, we found that the bacterial network of ROZ, which had more negative correlations, higher average connectivity, shorter average path length, and smaller modularity, was more complex than the network of CDZ. This suggested that the bacterial community was more stable and less vulnerable to change in the ROZ habitat than in the CDZ habitat. Overall, our findings suggest that the heterogeneity of soil properties and plant community collectively affect the structure of the soil bacterial community in an arid inland river basin. However, the influence of plant functional traits on the variation of the bacterial community depends on soil properties and plant community.

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Microbial Diversity in an Arid, Naturally Saline Environment

Cited by 38 publications

References 51 publications

Assessment of 16S rRNA Gene-Based Phylogenetic Diversity of Archaeal Communities in Halite-Crystal Salts Processed from Natural Saharan Saline Systems of Southern Tunisia

Assessment of 16S rRNA Gene-Based Phylogenetic Diversity of Archaeal Communities in Halite-Crystal Salts Processed from Natural Saharan Saline Systems of Southern Tunisia

Impact of a Nature-Inspired Engineered Soil Structure on Microbial Diversity and Community Composition in the Bulk Soil and Rhizosphere of Tomato Grown Under Saline Irrigation Water

Soil Property and Plant Diversity Determine Bacterial Turnover and Network Interactions in a Typical Arid Inland River Basin, Northwest China

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