Microbiology of Extreme Soils: 13 (Soil Biology)

Professor Brajesh Singh (Director, Global Centre for Land-Based Innovation)

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Pages Extreme Views on Prokaryote Evolution. Biodiversity: Extracting Lessons from Extreme Soils. Halophilic and Halotolerant Micro-Organisms from Soils.

Carmen Marquez. Atacama Desert Soil Microbiology. Rainey, Kimberley A. Warren-Rhodes, Christopher P.

Niall A. Logan A. Logan, Raymond N. Allan N. Peatland Microbiology.

Subsurface Geomicrobiology of the Iberian Pyritic Belt. Lucas A. Ruberto, Susana C. Vazquez, Walter P. No significant changes in the total ribosomal count was detected except in the first sample taken during severe desiccation, which showed an order of magnitude decrease in ribosomal count. While the total abundance remained stable, the relative abundance exhibited dynamic changes following the rainfall event Fig. Observed is that several taxa became dominant for the first few days after the rainfall Enterobacterales, Clostridiales, Lactobacillales and Bacteroidales.

Subsequently, these dominant classes slowly declined in the ensuing soil desiccation.

Some of these, specifically Clostridiales, Lactobacillales and Bacteroidales are known to include many anaerobic species 30 implying that some niches in the saturated desert soil have become anaerobic. A The dynamics of relative abundance of soil microbial classes during the field observations. Each time point is an average of three biological replicates.

The Biology of Arid Soils

Time zero is an average of three samples taken from fully desiccated soil during the summer of The size of the symbol corresponds to the water content measured in the soil at the time of sampling. The changes in the relative abundances of soil microbial taxa reflect drastic and rapid changes in microbial community composition. To track the shift in the microbial communities during the wetting and drying cycle, we performed a non-metric multidimensional scaling Fig.

Three distinct communities emerged: one orange squares consisting of a microbial community in desiccated desert soil low hydration conditions , a second blue triangles clustering the communities in very wet soil the saturation degree is about 0. Moreover, soil communities were grouped according to time of sampling: samples collected during low hydration conditions time zero, days 1, 8, 10 and 14 , high hydration days 2, 4 and 6 and intermediate hydration conditions days 6 and 8 , formed separate clusters, quantitatively.

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This implies that the main component of the community before the rain event and after the desiccation was not affected. The variations in relative abundance were translated to changes in soil microbial diversity. In Fig. In the field, we monitored three adjacent plots concomitantly; minute differences in their desiccation rates instigated observable differences in the community Fig. For example, the soil in plot 3 marked as yellow in the figure dried relatively faster than in plots 1 and 2, possibly leading to earlier onset of changes in microbial diversity in the plot.

The trend line is the averaged value of the data. The measured gravimetric water content of each plot in corresponding colours and the averaged values are given in C. The model results were in qualitative agreement with field observations in terms of microbial diversity and the community composition changes.

Figure 3 depicts the predicted effect of hydration dynamics on the soil microbial community. After soil wetting, the relative abundance of various taxa exhibited a dynamic response. Figure 3A shows the rise of anaerobic classes marked with strong colours from day 2 to day 7, replacing aerobic classes that were prevalent in the dry soil. The model results show the sharp decrease of anaerobes at between day 6 and day 7 as the soil became aerated again. While drying, air penetrates through the profile and shifts most of the domain back from anoxic to oxic conditions corresponding to a water content of 0.

Furthermore, in Fig. The decrease in diversity indicates the rises of dominant taxa during wetting. This is driven by competitive interactions among individuals over a common substrate, in this case the carbon source.

Tiny cells may best survive hot soils

The connected aqueous habitats and the increased dispersal of cells allowed intense competition for the substrate thereby causing the changes in diversity. The recovery of diversity reflects the role of aqueous habitat fragmentation. As the degree of connectivity in the aqueous phase decreased, microbial interactions are spatially limited Essentially, the observed dynamics of community composition and diversity are the outcome of simultaneous effects of the competition over dissolved substrates and the temporary dominance of anaerobic taxa due the transition from oxic to anoxic conditions in some parts of the wet soil.

A The relative abundance dynamics of modelled bacterial classes are depicted. In the simulations, 40 virtual taxa 20 taxa growing aerobically and other 20 taxa growing anaerobically were inoculated.

Breadcrumb

For this figure, the virtual taxa were classified to 10 classes 5 aerobic groups shown in light colours and 5 anaerobic groups shown in dark colours and the relative abundance dynamics of 10 independent simulations were averaged. B Shannon index of the simulated bacterial populations were compared with the field measurements suggesting that in both the diversity decreased rapidly after wetting and then recovered with drying.

For this comparison, the field measurements and the simulation results were rescaled with the value at day 0 dry soil indicating the relative changes. Results from 10 individual simulations with different inoculation of microbial cells and different soil structures with same pore size distribution and porosity are averaged red line and shaded area in pink indicates the standard deviation s.

Several studies have followed soil microbial communities in situ measuring their diversity and community composition following wetting events 21 , 32 , The findings generally support higher microbial diversity or coexistence degree under drier conditions where the aqueous-phase is largely fragmented and dispersion is limited. In previous studies, hydration conditions were under controlled laboratory experiments 9 , 10 , 17 , 24 , and in the field following the first rainfall after a prolonged draught 18 , 24 , In contrast with such a step-change in hydration conditions, the dynamics of soil microbial diversity during a cycle of wetting and gradual desiccation received little attention.

Here, we provide a detailed account of microbial response to wetting and subsequent drying in desert soil in the field and using a mechanistic model. We quantified soil microbial community composition in desert before, during, and after a major rain event.

Microbial community dynamics deduced from field observations were compared with results of the mechanistic model that simulated substrate diffusion and growth of multi-taxa microbial communities on idealised hydrated soil profile. The field observations and modelling results yield similar temporal dynamics of microbial diversity and community composition during hydration-desiccation cycles. The model focuses on the putative role of aqueous phase connectivity.

Following soil wetting, the increased connectivity of habitats facilitates higher rates of substrate diffusion and larger ranges of cell dispersion as key mechanisms for the observed loss of diversity during wetting 31 , Furthermore, the detailed account of water configuration dynamics in the soil profile and associated oxygen diffusion suggest the possibility of establishing anoxic conditions following wetting that may last a day or two within the soil volume.

Notably, the extensive changes in diversity were not reflected in the abundance of active microorganisms Figure S2 , this is in agreement with previous studies that show no changes in soil bacterial abundance with hydration following a long drought 9 , 10 , The soil community composition was significantly altered after a large rainfall event Fig. Some of the observed changes under field conditions could have resulted from dispersal and establishment of other migrated taxa during desiccation.

Yet, in the model such dispersal processes were minor, and the resulting diversity patterns were similar to field observations Fig.

INTRODUCTION

Moreover, the nMDS suggest that the community composition had returned to pre-rainfall composition Fig. This supports that immigration effect during and after wetting is questionable. We thus conclude that although dispersal and migration could contribute to changes in community composition, they are probably not the main factors in this complex ecosystem. A factor that may have contributed to the changes in microbial community composition was the formation of anoxic regions in the soil following the rainfall 35 , Such episodic increase in anaerobic taxa with the onset of anoxic conditions has been shown in previous studies 37 and their occurrence was coincidental to increase fluxes of carbon and nitrogen 35 , 38 , The carbon flux is introduced with precipitation from the carbon fixing soil crust in this system This results in an increase of available organic carbon in the top soil profile during days 1—3 Figure S1g.

This was represented in the model by the substrate entering to the system given as the constant concentration boundary condition on the top of the domain.

SSS1 – History, Education and Society of Soil Science

Mass flux, however, is elevated during wetting due to greater water film thickness See SI Text 4. Heterotrophic organisms utilise this fixed carbon source for their activity. Since metabolism in anoxic environments requires different terminal electron acceptors, nitrate respiration is expected. The soil nitrate pool increases during dry periods and this will be available for anaerobes together with carbon sources right after the wetting Changes in total nitrate Figure S1d support the postulated increase in anaerobic activity On the other hand, total ammonia shows a complementary behaviour to nitrate Figure S1b owing to the suppressed aerobic activity as aerobic metabolism requires ammonia as the nitrogen source.

We note that it is not clear where the ammonia flux comes from. It could be either nitrogen fixing bacteria on the crust or a deposited source at the surface introduced by the rainfall event.

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