Seasonal and spatial variability in total and active bacterial communities from desert soil

Baubin, Capucine; Farrell, Arielle M.; Šťovíček, Adam; Ghazaryan, Lusine; Giladi, Itamar; Gillor, Osnat

doi:10.1016/j.pedobi.2019.02.001

Cited by 25 publications

(28 citation statements)

References 43 publications

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“…The five most abundant bacteria in surrounding soils were WD2101 (the Phycisphaerae order), Sphingomonas , Solirubrobacter , Arthrobacter , and JG30-KF-CM45; while Halotalea, Crinalium , Niastella, Sediminibacter and several members of the Cyanobacteria phylum were unique to it. The soil bacterial community was qualitatively similar to what was found in a previous study in the same region of the Negev Desert [39] (Additional file 1: Appendix B).…”

Section: Resultssupporting

confidence: 81%

Gut bacteria of weevils developing on plant roots under extreme desert conditions

et al. 2019

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BackgroundMany phytophagous insects, whose diet is generally nitrogen-poor, rely on gut bacteria to compensate for nutritional deficits. Accordingly, we hypothesized that insects in desert environments may evolve associations with gut bacteria to adapt to the extremely low nutrient availability. For this, we conducted a systematic survey of bacterial communities in the guts of weevils developing inside mud chambers affixed to plant roots in the Negev Desert of Israel, based on 16S rRNA gene amplicon sequencing.ResultsOur analyses revealed that gut bacterial communities in weevil larvae were similar across a wide geographical range, but differed significantly from those of the mud chambers and of the surrounding soils. Nevertheless, a high proportion of bacteria (including all of the core bacteria) found in the weevils were also detected in the mud chambers and soils at low relative abundances. The genus Citrobacter (of the Enterobacteriaceae family) was the predominant group in the guts of all individual weevils. The relative abundance of Citrobacter significantly decreased at the pupal and adult stages, while bacterial diversity increased. A mini literature survey revealed that members of the genus Citrobacter are associated with nitrogen fixation, recycling of uric acid nitrogen, and cellulose degradation in different insects.ConclusionsThe results suggest that although weevils could potentially acquire their gut bacteria from the soil, weevil host internal factors, rather than external environmental factors, were more important in shaping their gut bacterial communities, and suggest a major role for Citrobacter in weevil nutrition in this challenging environment. This study highlights the potential involvement of gut bacteria in the adaptation of insects to nutritional deficiencies under extreme desert conditions.

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Section: Resultssupporting

confidence: 81%

Gut bacteria of weevils developing on plant roots under extreme desert conditions

et al. 2019

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“…We previously demonstrated that the total and active communities in the Negev soil used in this study differ in both abundance profiles and community composition during the dry season, while during the wet season, no differences were detected (Baubin et al, 2019). During the dry season, a “phantom taxa” (Klein et al, 2016), Deinococcus-Thermus, comprised ≈30% of the total soil community (Baubin et al, 2019) but was undetected in the active community of the dry season by any of the methods used here. These results suggest that the DNA-based total community may differ from the RNA-based community and thus cannot be used as a reliable reference for diversity.…”

Section: Discussionmentioning

confidence: 78%

“…The mean annual precipitation at the sampling site is 90 mm and the mean annual temperature is 30° (LTER data). Samples were collected under the canopy of perennial shrub Hammada scoparia in October 2015 at the end of the dry season as previously described (Baubin et al, 2019). Briefly, sampling was conducted in seven random blocks, each providing two technical replicates resulting in 14 samples.…”

Section: Methodsmentioning

confidence: 99%

The effect of reverse transcription enzymes and conditions on high throughput amplicon sequencing of the 16S rRNA

Šťovíček

Cohen-Chalamish

Gillor

2019

PeerJ

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It is assumed that the sequencing of ribosomes better reflects the active microbial community than the sequencing of the ribosomal RNA encoding genes. Yet, many studies exploring microbial communities in various environments, ranging from the human gut to deep oceans, questioned the validity of this paradigm due to the discrepancies between the DNA and RNA based communities. Here, we focus on an often neglected key step in the analysis, the reverse transcription (RT) reaction. Previous studies showed that RT may introduce biases when expressed genes and ribosmal rRNA are quantified, yet its effect on microbial diversity and community composition was never tested. High throughput sequencing of ribosomal RNA is a valuable tool to understand microbial communities as it better describes the active population than DNA analysis. However, the necessary step of RT may introduce biases that have so far been poorly described. In this manuscript, we compare three RT enzymes, commonly used in soil microbiology, in two temperature modes to determine a potential source of bias due to non-standardized RT conditions. In our comparisons, we have observed up to six fold differences in bacterial class abundance. A temperature induced bias can be partially explained by G-C content of the affected bacterial groups, thus pointing toward a need for higher reaction temperatures. However, another source of bias was due to enzyme processivity differences. This bias is potentially hard to overcome and thus mitigating it might require the use of one enzyme for the sake of cross-study comparison.

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“…Sampling was conducted as previously described(Baubin et al, 2019) with slight modifications, such as the inclusion of Shrub&Nest samples. To summarize, we sampled four distinct patch types: (1) barren soil (Barren); (2) under the canopy of H. scoparia (Shrub); (3) 20-30 cm from the main opening of the nest of M. ebeninus (Nest); and (4) 20-30 cm from ant nest's opening that was situated under a shrub canopy (Shrub&Nest).…”

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confidence: 99%

The role of ecosystem engineers in shaping the diversity and function of arid soil bacterial communities

Baubin

Farrell

Šťovíček

et al. 2020

Preprint

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Ecosystem engineers (EEs) are present in every environment and are known to strongly influence ecological processes and thus shape the distribution of species and resources. In this study, we assessed the direct and indirect effect of two EEs (perennial shrubs and ant nests), individually and combined, on the composition and function of arid soil bacterial communities. To that end, top soil samples were collected in the Negev Desert Highlands during the dry season from four patch types: (1) barren soil; (2) under shrubs; (3) near ant nests; or (4) near ant nests situated under shrubs. The bacterial composition was evaluated in the soil samples (fourteen replicates per patch type) using 16S rRNA gene amplicon sequencing, together with physico-chemical measures of the soil, and the potential functions of the community. We have found that the EEs differently affected the community composition. Indeed, barren patches supported a soil microbiome, dominated by Rubrobacter and Proteobacteria, while in EE patches the Deinococcus-Thermus phylum was dominating. The presence of the EEs similarly enhanced the abundance of phototrophic, nitrogen cycle and stress- related genes. In addition, only when both EEs were combined, were the soil characteristics altered. Our results imply that arid landscapes foster unique communities selected by each EE(s), solo or in combination, yet these communities have similar potential biological traits to persist under the harsh arid conditions. Environments with multiple EEs are complicated to study due to the possibility of non-additive effects of EEs and thus further research should be done.IMPORTANCEEcosystem engineers are organisms that can create, modify, or maintain their habitat. They are present in various environments but are particularly conspicuous in desert ecosystems, where their presence is tightly linked to vital resources like water or nutrients. Despite their key role in structuring and controlling desert ecosystems, joint engineering, and their effect on soil function, are unknown. Our study explores the contributions of key ecosystem engineers to the diversity and function of their soil microbiome allowing better understanding of their role in shaping habitats and engineering their activity

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Seasonal and spatial variability in total and active bacterial communities from desert soil

Cited by 25 publications

References 43 publications

Gut bacteria of weevils developing on plant roots under extreme desert conditions

Gut bacteria of weevils developing on plant roots under extreme desert conditions

The effect of reverse transcription enzymes and conditions on high throughput amplicon sequencing of the 16S rRNA

The role of ecosystem engineers in shaping the diversity and function of arid soil bacterial communities

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