scholarly journals Chronic Physical Disturbance Substantially Alters the Response of Biological Soil Crusts to a Wetting Pulse, as Characterized by Metatranscriptomic Sequencing

2018 ◽  
Author(s):  
Blaire Steven ◽  
Cheryl R. Kuske
Keyword(s):  
Microbial Communities ◽  
Carbon Fixation ◽  
Metabolic Response ◽  
Soil Depth ◽  
Soil Microbial Communities ◽  
Biogeochemical Cycling ◽  
Transcript Abundance ◽  
Biological Soil Crusts ◽  
Surface Soils ◽  
Soil Crusts

AbstractBiological soil crusts (biocrusts) are microbial communities that are a feature of arid surface soils worldwide. In drylands where precipitation is pulsed and ephemeral, the ability of biocrust microbiota to rapidly initiate metabolic activity is critical to their survival. Community gene expression was compared after a short duration (1 hour) wetting pulse in both intact and soils disturbed by chronic foot trampling.Across the metatranscriptomes the majority of transcripts were cyanobacterial in origin, suggesting that cyanobacteria accounted for the bulk of the transcriptionally active cells. Chronic trampling substantially altered the functional profile of the metatranscriptomes, specifically resulting in a significant decrease in transcripts for nitrogen fixation. Soil depth (biocrust and below crust) was a relatively small factor in differentiating the metatranscriptomes, suggesting that the metabolically active bacteria were similar between shallow soil horizons. The dry samples were consistently enriched for hydrogenase genes, indicating that molecular hydrogen may serve as an energy source for the desiccated soil communities. The water pulse was associated with a restructuring of the metatranscriptome, particularly for the biocrusts. Biocrusts increased transcripts for photosynthesis and carbon fixation, suggesting a rapid resuscitation upon wetting. In contrast, the trampled surface soils showed a much smaller response to wetting, indicating that trampling altered the metabolic response of the community. Finally, several biogeochemical cycling genes in carbon and nitrogen cycling were assessed for their change in abundance due to wetting in the biocrusts. Different transcripts encoding the same gene product did not show a consensus response, with some more abundant in dry or wet biocrusts, highlighting the challenges in relating transcript abundance to biogeochemical cycling rates.These observations demonstrate that metatranscriptome sequencing was able to distinguish alterations in the function of arid soil microbial communities at two varying temporal scales, a long-term ecosystems disturbance through foot trampling, and a short term wetting pulse. Thus, community metatranscriptomes have the potential to inform studies on the response and resilience of biocrusts to various environmental perturbations.

scholarly journals Ecological and genomic attributes of novel bacterial taxa that thrive in subsurface soil horizons

2019 ◽  
Author(s):  
Tess E. Brewer ◽  
Emma L. Aronson ◽  
Keshav Arogyaswamy ◽  
Sharon A. Billings ◽  
Jon K. Botthoff ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Depth ◽  
Soil Microbial Communities ◽  
Soil Profiles ◽  
Growth Strategies ◽  
Surface Soils ◽  
Wide Range ◽  
Bacterial And Archaeal Communities ◽  
Archaeal Communities ◽  
The U.S

AbstractWhile most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the U.S. to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.ImportanceSoil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the U.S., we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored distinct communities compared to the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising amount of novel microbes with unique adaptations to oligotrophic subsurface conditions.

scholarly journals Comparison of Drivers of Soil Microbial Communities Developed in Karst Ecosystems with Shallow and Deep Soil Depths

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 173
Author(s):  
Huiling Guan ◽  
Jiangwen Fan ◽  
Haiyan Zhang ◽  
Warwick Harris
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Soil Depth ◽  
Phospholipid Fatty Acid ◽  
Soil Microbial Communities ◽  
Deep Soil ◽  
Soil System ◽  
Soil Microbial ◽  
Total Soil ◽  
Karst Ecosystems

Soil erosion is prevalent in karst areas, but few studies have compared the differences in the drivers for soil microbial communities among karst ecosystems with different soil depths, and most studies have focused on the local scale. To fill this research gap, we investigated the upper 20 cm soil layers of 10 shallow–soil depth (shallow–SDC, total soil depth less than 100 cm) and 11 deep–soil depth communities (deep–SDC, total soil depth more than 100 cm), covering a broad range of vegetation types, soils, and climates. The microbial community characteristics of both the shallow–SDC and deep–SDC soils were tested by phospholipid fatty acid (PLFAs) analysis, and the key drivers of the microbial communities were illustrated by forward selection and variance partitioning analysis. Our findings demonstrated that more abundant soil nutrients supported higher fungal PLFA in shallow–SDC than in deep–SDC (p < 0.05). Furthermore, stronger correlation between the microbial community and the plant–soil system was found in shallow–SDC: the pure plant effect explained the 43.2% of variance in microbial biomass and 57.8% of the variance in the ratio of Gram–positive bacteria to Gram–negative bacteria (G+/G−), and the ratio of fungi to total bacteria (F/B); the pure soil effect accounted for 68.6% variance in the microbial diversity. The ratio of microbial PLFA cyclopropyl to precursors (Cy/Pr) and the ratio of saturated PLFA to monounsaturated PLFA (S/M) as indicators of microbial stress were controlled by pH, but high pH was not conducive to microorganisms in this area. Meanwhile, Cy/Pr in all communities was >0.1, indicating that microorganisms were under environmental stress. Therefore, the further ecological restoration of degraded karst communities is needed to improve their microbial communities.

scholarly journals Soil microbial communities and elk foraging intensity: implications for soil biogeochemical cycling in the sagebrush steppe

2017 ◽  
Vol 20 (2) ◽  
pp. 202-211 ◽  
Author(s):  
Lauren C. Cline ◽  
Donald R. Zak ◽  
Rima A. Upchurch ◽  
Zachary B. Freedman ◽  
Anna R. Peschel
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Biogeochemical Cycling ◽  
Sagebrush Steppe ◽  
Soil Microbial

scholarly journals Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons

mBio ◽  
2019 ◽  
Vol 10 (5) ◽  
Author(s):  
Tess E. Brewer ◽  
Emma L. Aronson ◽  
Keshav Arogyaswamy ◽  
Sharon A. Billings ◽  
Jon K. Botthoff ◽  
...  
Keyword(s):  
United States ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
The United States ◽  
Soil Profiles ◽  
Growth Strategies ◽  
Surface Soils ◽  
Wide Range ◽  
Bacterial And Archaeal Communities ◽  
Archaeal Communities

ABSTRACT While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments. IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.

Biological soil crusts: new genera and species of Cyanobacteria from Brazilian semi-arid regions

Phytotaxa ◽  
2020 ◽  
Vol 470 (4) ◽  
pp. 263-281
Author(s):  
NÁTHALI MARIA MACHADO DE LIMA ◽  
LUIS H.Z. BRANCO
Keyword(s):  
Carbon Fixation ◽  
Phylogenetic Analyses ◽  
Close Relation ◽  
Biological Soil Crusts ◽  
Rrna Gene ◽  
New Genera ◽  
Filamentous Cyanobacteria ◽  
Soil Crusts ◽  
Code Of Nomenclature ◽  
Real Composition

In the uppermost millimeters of soils is commonly found a thin layer of cryptobiotic organisms, including cyanobacteria, microalgae, lichens, mosses, fungi, bacteria and archaea. These communities are called Biological Soil Crusts (BSCs) or biocrusts and perform important ecological functions, mainly attributed to their capacity of providing soil stability and incorporate nutrients through nitrogen and carbon fixation. Among all the organisms found in the biocrusts, the filamentous cyanobacteria Microcoleus vaginatus and M. steenstrupii are the best studied soil colonizers. The genus Microcoleus is considered complex and has been showing close relation with some species of Phormidium. The poor understanding about these two genera is a limit to the description of the real composition of biocrusts and can generate underestimations in the diversity community and the use of wrong organisms in applied projects (e.g. environmental restoration). This work studied eight cyanobacterial populations from Brazilian BSCs sampled in the Caatinga biome. The populations presented Microcoleus-like and Phormidium-like morphologies, but the phylogenetic analyses based on 16S rRNA gene sequences showed that they represent three new genera and six new species of filamentous cyanobacteria associated to the cryptic genera, they are Pycnacronema caatingensis sp. nov., Pycnacronema edaphica sp. nov., Gracilinea arenicola gen. et sp. nov., Marmoreocelis xerophila gen. et sp. nov., Konicacronema caatinguensis gen. et sp. nov. and Trichocoleus caatingensis sp. nov. The generic name and specific epithets of the new taxa are proposed according to the provisions of the International Code of Nomenclature of algae, fungi, and plants.

scholarly journals Soil-Borne Microbial Functional Structure across Different Land Uses

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Eiko E. Kuramae ◽  
Jizhong Z. Zhou ◽  
George A. Kowalchuk ◽  
Johannes A. van Veen
Keyword(s):  
Microbial Communities ◽  
Carbon Fixation ◽  
Gene Diversity ◽  
Soil Microbial Communities ◽  
Regression Tree ◽  
Functional Structure ◽  
Land Uses ◽  
Total N ◽  
Number Of Genes ◽  
Carbon Degradation

Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio. C : N ratio showed a significant positive correlation with clay and soil pH. Fields with low C : N ratio had an overrepresentation of genes for carbon degradation, carbon fixation, metal reductase, and organic remediation categories, while fields with high C : N ratio had an overrepresentation of genes encoding dissimilatory sulfate reductase, methane oxidation, nitrification, and nitrogen fixation. The most abundant genes related to carbon degradation comprised bacterial and fungal cellulases; bacterial and fungal chitinases; fungal laccases; and bacterial, fungal, and oomycete polygalacturonases. The high number of genes related to organic remediation was probably driven by high phosphate content, while the high number of genes for nitrification was probably explained by high total nitrogen content. The functional gene diversity found in different soils did not group the sites accordingly to land management. Rather, the soil factors, C : N ratio, phosphate, and total N, were the main factors driving the differences in functional genes across the fields examined.

scholarly journals Flux balance modeling to predict bacterial survival during pulsed-activity events

2018 ◽  
Vol 15 (7) ◽  
pp. 2219-2229 ◽  
Author(s):  
Nicholas A. Jose ◽  
Rebecca Lau ◽  
Tami L. Swenson ◽  
Niels Klitgord ◽  
Ferran Garcia-Pichel ◽  
...  
Keyword(s):  
Mass Spectroscopy ◽  
Compatible Solutes ◽  
Soil Microbial Communities ◽  
Metabolic Model ◽  
Biological Soil Crusts ◽  
Arid Environments ◽  
Bacterial Survival ◽  
Flux Balance ◽  
Soil Crusts ◽  
Microcoleus Vaginatus

Abstract. Desert biological soil crusts (BSCs) are cyanobacteria-dominated surface soil microbial communities common to plant interspaces in arid environments. The capability to significantly dampen their metabolism allows them to exist for extended periods in a desiccated dormant state that is highly robust to environmental stresses. However, within minutes of wetting, metabolic functions reboot, maximizing activity during infrequent permissive periods. Microcoleus vaginatus, a primary producer within the crust ecosystem and an early colonizer, initiates crust formation by binding particles in the upper layer of soil via exopolysaccharides, making microbial dominated biological soil crusts highly dependent on the viability of this organism. Previous studies have suggested that biopolymers play a central role in the survival of this organism by powering resuscitation, rapidly forming compatible solutes, and fueling metabolic activity in dark, hydrated conditions. To elucidate the mechanism of this phenomenon and provide a basis for future modeling of BSCs, we developed a manually curated, genome-scale metabolic model of Microcoleus vaginatus (iNJ1153). To validate this model, gas chromatography–mass spectroscopy (GC–MS) and liquid chromatography–mass spectroscopy (LC–MS) were used to characterize the rate of biopolymer accumulation and depletion in in hydrated Microcoleus vaginatus under light and dark conditions. Constraint-based flux balance analysis showed agreement between model predictions and experimental reaction fluxes. A significant amount of consumed carbon and light energy is invested into storage molecules glycogen and polyphosphate, while β-polyhydroxybutyrate may function as a secondary resource. Pseudo-steady-state modeling suggests that glycogen, the primary carbon source with the fastest depletion rate, will be exhausted if M. vaginatus experiences dark wetting events 4 times longer than light wetting events.

Analyses of dryland biological soil crusts highlight lichens as an important regulator of microbial communities

2014 ◽  
Vol 23 (7) ◽  
pp. 1735-1755 ◽  
Author(s):  
Stefanie Maier ◽  
Thomas S. B. Schmidt ◽  
Lingjuan Zheng ◽  
Thomas Peer ◽  
Viktoria Wagner ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Biological Soil Crusts ◽  
Soil Crusts ◽  
Important Regulator
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