Optimizing the Production of Nursery-Based Biological Soil Crusts for Restoration of Arid Land Soils

Abstract

Biological soil crusts (biocrusts) are topsoil communities formed by cyanobacteria or other microbial primary producers and are typical of arid and semiarid environments. Biocrusts promote a range of ecosystem services, such as erosion resistance and soil fertility, but their degradation by often anthropogenic disturbance brings about the loss of these services. This has prompted interest in developing restoration techniques. One approach is to source biocrust remnants from the area of interest for scale-up cultivation in a microbial "nursery" that produces large quantities of high-quality inoculum for field deployment. However, growth dynamics and the ability to reuse the produced inoculum for continued production have not been assessed. To optimize production, we followed nursery growth dynamics of biocrusts from cold (Great Basin) and hot (Chihuahuan) deserts. Peak phototrophic biomass was attained between 3 and 7 weeks in cold desert biocrusts and at 12 weeks in those from hot deserts. We also reused the resultant biocrust inoculum to seed successive incubations, tracking both phototroph biomass and cyanobacterial community structure using 16S rRNA gene amplicon sequencing. Hot desert biocrusts showed little to no viability upon reinoculation, while cold desert biocrusts continued to grow, but at the expense of progressive shifts in species composition. This leads us to discourage the reuse of nursery-grown inoculum. Surprisingly, growth was highly variable among replicates, and overall yields were low, a fact that we attribute to the demonstrable presence of virulent and stochastically distributed but hitherto unknown cyanobacterial pathogens. We provide recommendations to avoid pathogen incidence in the process.IMPORTANCE Biocrust communities provide important ecosystem services for arid land soils, such as soil surface stabilization promoting erosion resistance and contributing to overall soil fertility. Anthropogenic degradation to biocrust communities (through livestock grazing, agriculture, urban sprawl, and trampling) is common and significant, resulting in a loss of those ecosystem services. Losses impact both the health of the native ecosystem and the public health of local populations due to enhanced dust emissions. Because of this, approaches for biocrust restoration are being developed worldwide. Here, we present optimization of a nursery-based approach to scaling up the production of biocrust inoculum for field restoration with respect to temporal dynamics and reuse of biological materials. Unexpectedly, we also report on complex population dynamics, significant spatial variability, and lower than expected yields that we ascribe to the demonstrable presence of cyanobacterial pathogens, the spread of which may be enhanced by some of the nursery production standard practices.

Keywords: 16S rRNA; biocrust; biocrust restoration; biological soil crust; cyanobacteria; degraded soils; drylands; erosion control; restoration; soil microbiome.

FIG 1

Growth dynamics of phototrophic biomass (as chlorophyll a areal concentration) during biocrust incubations. Phase A is shown on the far left of each panel. Successive phase B reinoculations are shown under shading and numbered. For each time point, box plots indicate upper and lower quartiles, and median values are shown as solid lines within the boxes. Whiskers denote upper and lower range, and asterisks denote outliers. For phase A, n = 6, except at t = 0, where n = 3. For reinoculation 2, n = 6 except at t = 0, where n = 3. For reinoculation 3, n = 4, and for 4, n = 3. Blue lines denote chlorophyll a content of field biocrusts used as original inoculum (n = 3), and red lines indicate chlorophyll a content at t = 0 (n = 3). Solid colored lines indicate mean values and dashed lines indicate one upper and one lower standard deviation of field biocrusts (n = 3).

FIG 2

Cyanobacterial community composition in hot desert biocrusts, based on 16S rRNA amplicon sequencing, in biocrusts collected from the field (field), from the phase A incubation (1), and those resulting from a second recurrent production (2).

FIG 3

Cyanobacterial community composition in cold desert biocrusts, based on 16S rRNA amplicon sequencing, in biocrusts collected from the field (field), from the phase A incubation (1), and those resulting from recurrent production according to round (2, 3, and 4).

FIG 4

2D MDS of cyanobacterial community composition based on 16S rRNA amplicon sequencing, in biocrusts collected from the field (field), from the phase A incubation (1), those resulting from recurrent production according to round (2), and for cold desert biocrusts (3 and 4).

FIG 5

Bioassay determination of virulence toward M. vaginatus PCC9802. Liquid cultures were inoculated with 0.2 g of biocrust soils, and the potential to kill M. vaginatus was determined visually after 5 and 12 days of incubation. Top photograph is a positive for virulence, bottom is a negative for virulence.