The Microbiology of Biological Soil Crusts

Unravelling the main mechanism responsible for nocturnal CO2 uptake by dryland soils

Soil respiration, or CO2 efflux from soil, is a crucial component of the terrestrial carbon cycle in climate models. Contrastingly, many dryland soils absorb atmospheric CO2 at night, but the exact mechanisms driving this uptake are actively debated. Here we used a mechanistic model with heuristic approaches to unravel the underlying processes of the observed patterns of soil-atmosphere CO2 fluxes. We show that the temperature drop during nighttime is the main driver of CO2 uptake by increasing CO2 solubility and local water pH of a thin water film on soil particle surfaces, providing favourable conditions for carbonate precipitation. Our data demonstrate that the nocturnal inorganic carbon absorption is a common soil process, but often offset by biological CO2 production. The uptake rates can be impacted by different successional stages of biocrusts that consume or produce CO2 and modify the pH of the soil water film, which can be maintained by non-rainfall water inputs, such as pore space condensation. Annual estimates of nocturnal carbon uptake, based on in situ continuous measurements at the soil level in drylands are still very scarce, but fluxes of up to several tens of g C m-2 y-1 have been reported, potentially accounting for a considerable fraction of the global residual terrestrial carbon sink.

Survival and rapid resuscitation permit limited productivity in desert microbial communities

Microbial activity in drylands tends to be confined to rare and short periods of rain. Rapid growth should be key to the maintenance of ecosystem processes in such narrow activity windows, if desiccation and rehydration cause widespread cell death due to osmotic stress. Here, simulating rain with 2H2O followed by single-cell NanoSIMS, we show that biocrust microbial communities in the Negev Desert are characterized by limited productivity, with median replication times of 6 to 19 days and restricted number of days allowing growth. Genome-resolved metatranscriptomics reveals that nearly all microbial populations resuscitate within minutes after simulated rain, independent of taxonomy, and invest their activity into repair and energy generation. Together, our data reveal a community that makes optimal use of short activity phases by fast and universal resuscitation enabling the maintenance of key ecosystem functions. We conclude that desert biocrust communities are highly adapted to surviving rapid changes in soil moisture and solute concentrations, resulting in high persistence that balances limited productivity.

Nimble vs. torpid responders to hydration pulse duration among soil microbes

Environmental parameters vary in time, and variability is inherent in soils, where microbial activity follows precipitation pulses. The expanded pulse-reserve paradigm (EPRP) contends that arid soil microorganisms have adaptively diversified in response to pulse regimes differing in frequency and duration. To test this, we incubate Chihuahuan Desert soil microbiomes under separate treatments in which 60 h of hydration was reached with pulses of different pulse duration (PD), punctuated by intervening periods of desiccation. Using 16S rRNA gene amplicon data, we measure treatment effects on microbiome net growth, growth efficiency, diversity, and species composition, tracking the fate of 370 phylotypes (23% of those detected). Consistent with predictions, microbial diversity is a direct, saturating function of PD. Increasingly larger shifts in community composition are detected with decreasing PD, as specialist phylotypes become more prominent. One in five phylotypes whose fate was tracked responds consistently to PD, some preferring short pulses (nimble responders; NIRs) and some longer pulses (torpid responders; TORs). For pulses shorter than a day, microbiome growth efficiency is an inverse function of PD, as predicted. We conclude that PD in pulsed soil environments constitutes a major driver of microbial community assembly and function, largely consistent with the EPRP predictions.

Induced and natural moss soil crusts accelerate the C, N, and P cycles of PbZn tailings

Nutrient deficiency is the primary obstacle in tailing ecological restoration besides high heavy metal content. Biological soil crusts (BSCs) are known for their C and N fixation capabilities and play a crucial role in soil P cycle. BSCs are widespread in tailings and provide a potential ecological restoration approach. In 2022, we carried out an on-site restoration on a PbZn tailing pond in Yunnan Province, China. BSCs were propagated by natural moss crust fragment inoculation. The induced moss crusts (IMCs) were monitored at 0, 45, 90, and 135 days and compared with natural moss crusts (NMCs). The chlorophyll-a content and abundance of biotic organisms increased over time, reaching a peak at 135 days and surpassing that of NMCs. Moss crusts increased the content of C, N, and P nutrients and enzyme activities in the 0.5 cm surface soil. They also reduced the DTPA-extractable Pb content. Moss crusts significantly increased the content of fulvic/humic and protein-like/polyphenol substances, thereby raising the humic index of soil dissolved organic matter (especially NMCs). Furthermore, moss crusts also raised the abundance of nitrification (AOB and Nsr), denitrification (narG, napA, qnorB, and nosZ), and P-cycling (gcd, appA, phoC, phoA, and phoD) genes, especially IMCs after a 135-day inoculation. NMCs exhibited higher moss abundance measured via eukaryotic photoautotrophs. Moss crusts increased photosynthetic bacteria abundance (e.g., Leptolyngbya and Nostocales) and reduced the dominance of chemoautotrophic bacteria, especially the dark sulfide oxidation bacteria (Betaproteobacteriales). This trend was more pronounced in NMCs. Overall, IMCs can recover the functions of NMCs, and in some cases (e.g., abundance and diversity of biotic community, soil nutrient and N & P cycle genes), even surpass them. Our research provides new insights into the tailing ecological restoration.

Ecophysiological performance of terrestrial diatoms isolated from biocrusts of coastal sand dunes

Terrestrial diatoms are widespread in a large variety of habitats and are regularly recorded in biocrusts. Although diatoms have long been known to live in terrestrial habitats, only a few studies have focused on their diversity of ecophysiology. Here we present a study on the ecophysiological performance of five terrestrial diatom cultures from biocrusts, which were collected in sand dunes of the German coast of the Baltic Sea. The sampling sites were selected along a gradient of human impacts on the dunes. The richness of diatom species, roughly estimated from permanent slides, was around 30 species per sampling site. The species abundance was calculated in the same way revealing a high proportion of broken diatom frustules. All diatom cultures established in the laboratory showed no photoinhibition and high oxygen production along a light gradient. The desiccation tolerance differed among the strains, with high recovery observed for Hantzschia abundans and Achnanthes coarctata and low to no recovery for Pinnularia borealis and Pinnularia intermedia. The maximum growth rate for most strains was between 25 and 30°C. These temperatures can be easily reached in their natural environments. Nevertheless, during short-term exposure to elevated temperatures, oxygen production was recorded up to 35°C. Interestingly, two of five diatom cultures (Hantzschia abundans and Pinnularia borealis) produced mycosporine-like amino acids. These UV-protective substances are known from marine diatoms but not previously reported in terrestrial diatoms.

BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event

Determining which microorganisms are active within soil communities remains a major technical endeavor in microbial ecology research. One promising method to accomplish this is coupling bioorthogonal non-canonical amino acid tagging (BONCAT) with fluorescence activated cell sorting (FACS) which sorts cells based on whether or not they are producing new proteins. Combined with shotgun metagenomic sequencing (Seq), we apply this method to profile the diversity and potential functional capabilities of both active and inactive microorganisms in a biocrust community after being resuscitated by a simulated rain event. We find that BONCAT-FACS-Seq is capable of discerning the pools of active and inactive microorganisms, especially within hours of applying the BONCAT probe. The active and inactive components of the biocrust community differed in species richness and composition at both 4 and 21 h after the wetting event. The active fraction of the biocrust community is marked by taxa commonly observed in other biocrust communities, many of which play important roles in species interactions and nutrient transformations. Among these, 11 families within the Firmicutes are enriched in the active fraction, supporting previous reports indicating that the Firmicutes are key early responders to biocrust wetting. We highlight the apparent inactivity of many Actinobacteria and Proteobacteria through 21 h after wetting, and note that members of the Chitinophagaceae, enriched in the active fraction, may play important ecological roles following wetting. Based on the enrichment of COGs in the active fraction, predation by phage and other bacterial members, as well as scavenging and recycling of labile nutrients, appear to be important ecological processes soon after wetting. To our knowledge, this is the first time BONCAT-FACS-Seq has been applied to biocrust samples, and therefore we discuss the potential advantages and shortcomings of coupling metagenomics to BONCAT to intact soil communities such as biocrust. In all, by pairing BONCAT-FACS and metagenomics, we are capable of highlighting the taxa and potential functions that typifies the microbes actively responding to a rain event.