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.

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

2017 ◽  
Author(s):  
Nicholas A. Jose ◽  
Rebecca Lau ◽  
Tami L. Swenson ◽  
Niels Klitgord ◽  
Ferran Garcia-Pichel ◽  
...  
Keyword(s):  
Compatible Solutes ◽  
Soil Microbial Communities ◽  
Metabolic Model ◽  
Biological Soil Crusts ◽  
Arid Environments ◽  
Bacterial Survival ◽  
Soil Microbial ◽  
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 fuelling metabolic activity in dark, hydrated conditions. To elucidate the mechanism of this phenomenon and provide a basis for future modelling of BSCs, we developed a manually-curated, genome-scale metabolic model of Microcoleus vaginatus (iNJ1153). To validate this model, GC/MS and 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 modelling suggests that glycogen, the primary carbon source with the fastest depletion rate, will be exhausted if M. vaginatus experiences dark wetting events four times longer than light wetting events.

scholarly journals Diazotrophic Community Structure and Function in Two Successional Stages of Biological Soil Crusts from the Colorado Plateau and Chihuahuan Desert

2004 ◽  
Vol 70 (2) ◽  
pp. 973-983 ◽  
Author(s):  
Chris M. Yeager ◽  
Jennifer L. Kornosky ◽  
David C. Housman ◽  
Edmund E. Grote ◽  
Jayne Belnap ◽  
...  
Keyword(s):  
Community Structure ◽  
Chihuahuan Desert ◽  
Nitrogenase Activity ◽  
Colorado Plateau ◽  
Biological Soil Crusts ◽  
Rrna Gene ◽  
Soil Crusts ◽  
Clone Sequencing ◽  
Microcoleus Vaginatus ◽  
Diazotrophic Community

ABSTRACT The objective of this study was to characterize the community structure and activity of N2-fixing microorganisms in mature and poorly developed biological soil crusts from both the Colorado Plateau and Chihuahuan Desert. Nitrogenase activity was approximately 10 and 2.5 times higher in mature crusts than in poorly developed crusts at the Colorado Plateau site and Chihuahuan Desert site, respectively. Analysis of nifH sequences by clone sequencing and the terminal restriction fragment length polymorphism technique indicated that the crust diazotrophic community was 80 to 90% heterocystous cyanobacteria most closely related to Nostoc spp. and that the composition of N2-fixing species did not vary significantly between the poorly developed and mature crusts at either site. In contrast, the abundance of nifH sequences was approximately 7.5 times greater (per microgram of total DNA) in mature crusts than in poorly developed crusts at a given site as measured by quantitative PCR. 16S rRNA gene clone sequencing and microscopic analysis of the cyanobacterial community within both crust types demonstrated a transition from a Microcoleus vaginatus-dominated, poorly developed crust to mature crusts harboring a greater percentage of Nostoc and Scytonema spp. We hypothesize that ecological factors, such as soil instability and water stress, may constrain the growth of N2-fixing microorganisms at our study sites and that the transition to a mature, nitrogen-producing crust initially requires bioengineering of the surface microenvironment by Microcoleus vaginatus.

Effects of inoculated Microcoleus vaginatus on the structure and function of biological soil crusts of desert

2010 ◽  
Vol 47 (4) ◽  
pp. 473-480 ◽  
Author(s):  
Yunpu Zheng ◽  
Ming Xu ◽  
Jiancheng Zhao ◽  
Shuqing Bei ◽  
Lihua Hao
Keyword(s):  
Biological Soil Crusts ◽  
Structure And Function ◽  
Soil Crusts ◽  
Microcoleus Vaginatus ◽  
And Function

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.

Distribution and Floristics of Bryophytes in Soil Crusts in Semi-Arid and Arid Eastern Australia

1996 ◽  
Vol 44 (2) ◽  
pp. 223 ◽  
Author(s):  
DJ Eldridge ◽  
ME Tozer
Keyword(s):  
Condition Assessment ◽  
Biological Soil Crusts ◽  
Arid Environments ◽  
Survey Area ◽  
Soil Crusts ◽  
Unpublished Studies ◽  
Eastern Australia ◽  
The Mean ◽  
Landscape Types ◽  
Semi Arid

A total of 56 bryophyte taxa associated with biological soil crusts was collected from 282 sites in semi-arid and arid eastern Australia. The 41 moss taxa and 15 liverwort taxa found were dominated by the families Pottiaceae and Ricciaceae respectively. Bryophytes were present at 224 of the 282 sites, and their distribution varied widely according to different landscapes. The mean number of taxa per site ranged from 8.9 on plains with red earths to 2.1 on active floodplains. The most common bryophytes found in the survey area were Bryum pachytheca, Didymodon torquatus, Gigaspermum repens, Goniomitrium enerve, Desmatodon convolutus, Stonea oleaginosa, Crossidium davidai, Riccia limbata and Riccia lamellosa. In this paper, the distribution of bryophytes in relation to landscape types, and some strategies for surviving in arid environments and their roles in biodiversity and rangeland condition assessment are discussed. Their distribution is compared with other published and unpublished studies from similar areas of Australia.

Small-scale patterns of abundance of mosses and lichens forming biological soil crusts in two semi-arid gypsum environments

2006 ◽  
Vol 54 (4) ◽  
pp. 339 ◽  
Author(s):  
I. Martínez ◽  
A. Escudero ◽  
F. T. Maestre ◽  
A. de la Cruz ◽  
C. Guerrero ◽  
...  
Keyword(s):  
Biological Soil Crust ◽  
Aggregate Stability ◽  
Bare Soil ◽  
Biological Soil Crusts ◽  
Small Scale ◽  
Arid Environments ◽  
Soil Variables ◽  
Constrained Ordination ◽  
Soil Crusts ◽  
Semi Arid

Despite important advances in the understanding of biological soil crusts and their key role in ecosystem processes in arid and semi-arid environments, little is known about those factors driving the small-scale patterns of abundance and distribution of crust-forming lichens and mosses. We used constrained ordination techniques (RDAs) to test the hypothesis that the spatial patterning of lichens and mosses is related to surface and subsurface soil variables in two semi-arid gypsum environments of Spain. Our results show that the abundance of mosses and lichens forming biological soil crusts was related to a limited set of variables (cover of bare soil and litter, soil respiration, potassium content and aggregate stability). Moreover, they provide some insights into the importance of these variables as drivers of biological soil-crust composition and abundance in semi-arid gypsum environments.

Discussion on wind factor influencing the distribution of biological soil crusts on surface of sand dunes

2013 ◽  
Vol 5 (6) ◽  
pp. 739
Author(s):  
Wu YongSheng ◽  
Erdun Hasi ◽  
Yin RuiPing ◽  
Zhang Xin ◽  
Ren Jie ◽  
...  
Keyword(s):  
Sand Dunes ◽  
Biological Soil Crusts ◽  
Soil Crusts

scholarly journals Soil microbial diversity–biomass relationships are driven by soil carbon content across global biomes

2021 ◽  
Author(s):  
Felipe Bastida ◽  
David J. Eldridge ◽  
Carlos García ◽  
G. Kenny Png ◽  
Richard D. Bardgett ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Soil Carbon ◽  
Soil Microbial Communities ◽  
Ecosystem Functions ◽  
Arid Environments ◽  
Soil Microbial Diversity ◽  
Soil Biodiversity ◽  
Soil C ◽  
Soil Microbial ◽  
Biomass Ratio

AbstractThe relationship between biodiversity and biomass has been a long standing debate in ecology. Soil biodiversity and biomass are essential drivers of ecosystem functions. However, unlike plant communities, little is known about how the diversity and biomass of soil microbial communities are interlinked across globally distributed biomes, and how variations in this relationship influence ecosystem function. To fill this knowledge gap, we conducted a field survey across global biomes, with contrasting vegetation and climate types. We show that soil carbon (C) content is associated to the microbial diversity–biomass relationship and ratio in soils across global biomes. This ratio provides an integrative index to identify those locations on Earth wherein diversity is much higher compared with biomass and vice versa. The soil microbial diversity-to-biomass ratio peaks in arid environments with low C content, and is very low in C-rich cold environments. Our study further advances that the reductions in soil C content associated with land use intensification and climate change could cause dramatic shifts in the microbial diversity-biomass ratio, with potential consequences for broad soil processes.

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