Common and distinguishing features of the bacterial and fungal communities in biological soil crusts and shrub root zone soils

Steven, Blaire; Gallegos‐Graves, La Verne; Yeager, Chris M.; Belnap, Jayne; Kuske, Cheryl R.

doi:10.1016/j.soilbio.2013.11.008

Cited by 92 publications

(83 citation statements)

References 70 publications

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“…2D and 3). Interestingly, the four functional metagenome categories whose members were found to be reduced in number in the IRW treatment plots were the same as those found in a previous study documenting the differences in bacterial communities in biocrusts and uncrusted soils in creosote bush root zones (24). This suggests that the functional effects of reductions in Cyanobacteria abundance are similar whether the reductions were induced by environmental perturbations or natural variance due to their proximity to local vegetation.…”

Section: Discussionsupporting

confidence: 80%

“…Quantitative PCR (qPCR) measured the abundance of bacterial 16S rRNA genes and was used as a proxy for total bacterial biomass. Bacterial qPCR was performed with primers EUB 338 (5=-ACT CCTACGGGAGGCAGCAG-3=) (22) and EUB 518 (5=-ATTACCGCGG CTGCTGG-3=), which target the V2 and V3 variable regions (23), and previously described amplification conditions (24). Chlorophyll a concentrations were used as a measure of Cyanobacteria biomass (25) and were determined by the procedure described by Castle et al (26).…”

Section: Methodsmentioning

confidence: 99%

“…The DNA templates from each sample were normalized to 1 ng l Ϫ1 , and gene fragments were amplified with the primers V5-forward (5=-RGGATTAGATACCC-3=) and V6-reverse (5=-CGACRR CCATGCANCACCT-3=) (29), with 8-bp barcodes included on the reverse primer for sample indexing (30). The amplification and cycling conditions were as described previously (24). Amplicon sequencing was performed using 454 FLX titanium chemistry.…”

Section: Methodsmentioning

confidence: 99%

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Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities

Steven

Kuske

Gallegos‐Graves

et al. 2015

Appl Environ Microbiol

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bBiological soil crusts (biocrusts) colonize plant interspaces in many drylands and are critical to soil nutrient cycling. Multiple climate change and land use factors have been shown to detrimentally impact biocrusts on a macroscopic (i.e., visual) scale. However, the impact of these perturbations on the bacterial components of the biocrusts remains poorly understood. We employed multiple long-term field experiments to assess the impacts of chronic physical (foot trampling) and climatic changes (2°C soil warming, altered summer precipitation [wetting], and combined warming and wetting) on biocrust bacterial biomass, composition, and metabolic profile. The biocrust bacterial communities adopted distinct states based on the mechanism of disturbance. Chronic trampling decreased biomass and caused small community compositional changes. Soil warming had little effect on biocrust biomass or composition, while wetting resulted in an increase in the cyanobacterial biomass and altered bacterial composition. Warming combined with wetting dramatically altered bacterial composition and decreased Cyanobacteria abundance. Shotgun metagenomic sequencing identified four functional gene categories that differed in relative abundance among the manipulations, suggesting that climate and land use changes affected soil bacterial functional potential. This study illustrates that different types of biocrust disturbance damage biocrusts in macroscopically similar ways, but they differentially impact the resident soil bacterial communities, and the communities' functional profiles can differ depending on the disturbance type. Therefore, the nature of the perturbation and the microbial response are important considerations for management and restoration of drylands.

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Section: Discussionsupporting

confidence: 80%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities

Steven

Kuske

Gallegos‐Graves

et al. 2015

Appl Environ Microbiol

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“…Microbial communities have been considered as principal drivers in nutrient cycling processes (Singh et al, 2010), and their competition with plants for limited nutrients will ultimately determine the sustainability of NPP in drylands. A number of Free-air CO 2 enrichment (FACE) experiments have been carried out to assess effects of climate change on dryland ecosystem functioning and nutrient cycling (Del Galdo et al, 2006;Jin and Evans, 2007;Steven et al, 2013), which revealed complex responses of soil microbial communities to the projected climate change. Despite the global distribution of drylands and their important ecosystem services, considerable uncertainty remains about how future climatic scenarios will affect the microbe-mediated nutrient cycling in these ecosystems.…”

Section: Introductionmentioning

confidence: 99%

Effects of climate warming and elevated CO 2 on autotrophic nitrification and nitrifiers in dryland ecosystems

Macdonald

Trivedi

et al. 2016

Soil Biology and Biochemistry

109

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a b s t r a c tGlobal climate change is predicted to enhance atmospheric temperature and CO 2 , with important consequences on biogeochemical nitrogen cycling in dryland ecosystems, which are highly vulnerable and characterized by extremely low nutrient availability. Belowground nitrification processes, predominantly mediated by ammonia-oxidizing archaea (AOA) and bacteria (AOB), are central to plant nitrogen availability and soil N 2 O emissions, but their responses to future climatic scenarios in drylands remain largely unknown. Here we investigated the impact of factorial combinations of elevated CO 2 (þ200 ppm) and elevated temperature (þ3 C) on dynamics of ammonia oxidizers and nitrification in three dryland soils planted with Eucalyptus tereticornis. Soil properties (including total carbon, H 2 O%, and nitrate) and potential nitrification rates were strongly impacted by elevated temperature after nine months, accompanied by significantly higher AOA abundance in two soils and a gradual decrease in AOB abundance under elevated temperature. DNA-stable isotope probing showed increased assimilation of 13 CO 2 by AOA, but not AOB, under warming, indicating that AOA were actively growing and utilizing the 13 CO 2 substrates, which was coupled with significantly higher net nitrogen mineralization and nitrification rates. High-throughput microarray analysis revealed temperature selections of particular AOA assemblages and a significant reduction in diversity and co-occurrence of the metabolically active AOA phylotypes. Although these responses were soil specific, structural equation modelling by compiling all the data together showed that warming had significant direct and indirect impacts on soil nitrification which were driven by changes in AOA community structure, but no obvious effects of elevated CO 2 could be identified. Our findings suggest that warming has stronger effects than elevated CO 2 on autotrophic nitrification, and AOA are more responsive to elevated temperature than AOB in the tested dryland ecosystems.

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“…Community profiling techniques such as denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) were initially used [for bacteria, see Garcia-Pichel et al (2001), Kuske et al (2002), Garcia-Pichel et al (2003), Yeager et al (2004), Nagy et al (2005), Gundlapally and Garcia-Pichel (2006), and Castillo-Monroy et al (2011); for fungi, see Bates and Garcia-Pichel (2009) and Bates et al (2012)]. Furthermore, 16S ribosomal RNA (rRNA) gene clone libraries were applied [for bacteria, see Yeager et al (2004), Gundlapally and Garcia-Pichel (2006), Yeager et al (2007), Abed et al (2010), and Moquin et al (2012); for bacteria and fungi, see Steven et al (2014)]. With the improvement of sequencing technologies such as highthroughput 16S rRNA gene sequence analyses and shotgun metagenome sequencing, there has been a resurgent interest in a wider characterization of the biocrust microbial communities (Steven et al 2012a(Steven et al , b, 2013a(Steven et al , b, 2014Angel and Conrad 2013;Davies et al 2013;Büdel et al 2014;Elliott et al 2014;Steven et al 2015).…”

mentioning

confidence: 99%

Bacteria and Non-lichenized Fungi Within Biological Soil Crusts

Maier

Muggia

Kuske

et al. 2016

Biological Soil Crusts: An Organizing Principle in Drylands

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Common and distinguishing features of the bacterial and fungal communities in biological soil crusts and shrub root zone soils

Cited by 92 publications

References 70 publications

Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities

Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities

Effects of climate warming and elevated CO 2 on autotrophic nitrification and nitrifiers in dryland ecosystems

Bacteria and Non-lichenized Fungi Within Biological Soil Crusts

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