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.

Years After a Fire, Biocrust Microbial Communities are Similar to Unburned Communities in a Coastal Grassland

Microbial communities are integral for ecosystem processes and their taxonomic composition and function may be altered by a disturbance such as fire. Biocrusts are composed of macroscopic and microscopic organisms and are important for a variety of ecosystem functions, such as nutrient cycling and erosion control. We sought to understand if biocrust community composition and function were altered 1 year after a prescribed fire and 6 years after a wildfire in a coastal California grassland on San Clemente Island. We used shotgun metagenomic sequencing and measurements of chlorophyll content, exopolysaccharide production related to soil stability, and nitrogen fixation. There were no differences in the community composition between unburned samples and the samples burned in the prescribed fire and wildfire. Chlorophyll content differed between the prescribed fire and the controls; however, there were no measured differences in exopolysaccharide production, and nitrogen fixation. However, the wildfire and their respective unburned samples had different functions based on the gene annotations. We compiled one Actinobacteria metagenome-assembled genome from the shotgun sequences which had genes for oxidative and heat stress tolerance. These results suggest that the biocrust community can reach a community composition and function similar to the unburned biocrusts within a year after a prescribed burn and 6 years after a wildfire. However, legacy effects of the wildfire may present themselves in the differences between functional gene sequences. Due to their ability to match the undisturbed community composition and function within years and without intervention, future restoration work should consider the biocrusts in their restoration plans as they may provide valuable ecosystem functions after a disturbance.

Fire and Rhizosphere Effects on Bacterial Co-Occurrence Patterns

Fires are common in Mediterranean soils and constitute an important driver of their evolution. Although fire effects on vegetation dynamics are widely studied, their influence on the assembly rules of soil prokaryotes in a small-scale environment has attracted limited attention. In the present study, we reanalyzed the data from Aponte et al. (2022) to test whether the direct and/or indirect effects of fire are reflected in the network of relationships among soil prokaryotes in a Chilean sclerophyllous ecosystem. We focused on bacterial (genus and species level) co-occurrence patterns in the rhizospheres and bulk soils in burned and unburned plots. Four soils were considered: bulk-burnt (BB), bulk-unburnt (BU), rhizosphere-burnt (RB), and rhizosphere-unburnt (RU). The largest differences in network parameters were recorded between RU and BB soils, while RB and BU networks exhibited similar values. The network in the BB soil was the most compact and centralized, while the RU network was the least connected, with no central nodes. The robustness of bacterial communities was enhanced in burnt soils, but this was more pronounced in BB soil. The mechanisms mainly responsible for bacterial community structure were stochastic in all soils, whether burnt or unburnt; however, communities in RB were much more stochastic than in RU.

Using simulated wildland fire to assess microbial survival at multiple depths from biocrust and bare soils

Introduction

Surface soil microbial communities are directly exposed to the heat from wildland fires. Due to this, the microbial community composition may be stratified within the soil profile with more heat tolerant microbes near the surface and less heat tolerant microbes, or mobile species found deeper in the soil. Biological soil crusts, biocrusts, are found on the soil surface and contain a diverse microbial community that is directly exposed to the heat from wildland fires.

Methods

Here, we used a simulated fire mesocosm along with a culture-based approach and molecular characterization of microbial isolates to understand the stratification of biocrust and bare soil microbes after low severity (450°C) and high severity (600°C) fires. We cultured and sequenced microbial isolates from 2 to 6 cm depth from both fire types.

Results

The isolates were stratified along the soil depth. Green algal isolates were less thermotolerant and found in the deeper depths (4–6 cm) and the control soils, while several cyanobacteria in Oscillatoriales, Synechococcales, and Nostocales were found at 2–3 cm depth for both fire temperatures. An Alphaproteobacteria isolate was common across several depths, both fire types, and both fire temperatures. Furthermore, we used RNA sequencing at three depths after the high severity fire and one control to determine what microbial community is active following a fire. The community was dominated by Gammaproteobacteria, however some Cyanobacteria ASVs were also present.

Discussion

Here we show evidence of stratification of soil and biocrust microbes after a fire and provide evidence that these microbes are able to survive the heat from the fire by living just below the soil surface. This is a steppingstone for future work on the mechanisms of microbial survival after fire and the role of soil insulation in creating resilient communities.

Divergence of Biocrust Active Bacterial Communities in the Negev Desert During a Hydration-Desiccation Cycle

Rain events in arid environments are highly unpredictable and intersperse extended periods of drought. Therefore, tracking changes in desert soil bacterial communities during rain events, in the field, was seldom attempted. Here, we assessed rain-mediated dynamics of active bacterial communities in the Negev Desert biological soil crust (biocrust). Biocrust samples were collected during, and after a medium rainfall and dry soil was used as a control; we evaluated the changes in active bacterial composition, potential function, potential photosynthetic activity, and extracellular polysaccharide (EPS) production. We hypothesized that rain would activate the biocrust phototrophs (mainly Cyanobacteria), while desiccation would inhibit their activity. In contrast, the biocrust Actinobacteria would decline during rewetting and revive with desiccation. Our results showed that hydration increased chlorophyll content and EPS production. As expected, biocrust rewetting activated Cyanobacteria, which replaced the former dominant Actinobacteria, boosting potential autotrophic functions. However, desiccation of the biocrust did not immediately change the bacterial composition or potential function and was followed by a delayed decrease in chlorophyll and EPS levels. This dramatic shift in the community upon rewetting led to modifications in ecosystem services. We propose that following a rain event, the response of the active bacterial community lagged behind the biocrust water content due to the production of EPS which delayed desiccation and temporarily sustained the biocrust community activity.

Biological Crusts to Increase Soil Carbon Sequestration: New Challenges in a New Environment

The major priority of research in the present day is to conserve the environment by reducing GHG emissions. A proposed solution by an expert panel from 195 countries meeting at COP 21 was to increase global SOC stocks by 0.4% year−1 to compensate for GHG emissions, the ‘4 per 1000′ agreement. In this context, the application of biocrusts is a promising framework with which to increase SOC and other soil functions in the soil–plant continuum. Despite the importance of biocrusts, their application to agriculture is limited due to: (1) competition with native microbiota, (2) difficulties in applying them on a large scale, (3) a lack of studies based on carbon (C) balance and suitable for model parameterization, and (4) a lack of studies evaluating the contribution of biocrust weathering to increase C sequestration. Considering these four challenges, we propose three perspectives for biocrust application: (1) natural microbiome engineering by a host plant, using biocrusts; (2) quantifying the contribution of biocrusts to C sequestration in soils; and (3) enhanced biocrust weathering to improve C sequestration. Thus, we focus this opinion article on new challenges by using the specialized microbiome of biocrusts to be applied in a new environment to counteract the negative effects of climate change.

Fine-Scale Spatial Structure of Soil Microbial Communities in Burrows of a Keystone Rodent Following Mass Mortality

Soil microbial communities both reflect and influence biotic and abiotic processes occurring at or near the soil surface. Ecosystem engineers that physically alter the soil surface, such as burrowing ground squirrels, are expected to influence the distribution of soil microbial communities. Black-tailed prairie dogs (Cynomys ludovicianus) construct complex burrows in which activities such as nesting, defecating, and dying are partitioned spatially into different chambers. Prairie dogs also experience large-scale die-offs due to sylvatic plague, caused by the bacterium Yersinia pestis, which lead to mass mortality events with potential repercussions on microbial communities. We used 16S sequencing to examine microbial communities in soil that was excavated by prairie dogs from different burrow locations, and surface soil that was used in the construction of burrow entrances, in populations that experienced plague die-offs. Following the QIIME2 pipeline, we assessed microbial diversity at several taxonomic levels among burrow regions. To do so, we computed community similarity metrics (Bray–Curtis, Jaccard, and weighted and unweighted UniFrac) among samples and community diversity indexes (Shannon and Faith phylogenetic diversity indexes) within each sample. Microbial communities differed across burrow regions, and several taxa exhibited spatial variation in relative abundance. Microbial ecological diversity (Shannon index) was highest in soil recently excavated from within burrows and soils associated with dead animals, and was lowest in soils associated with scat. Phylogenetic diversity varied only marginally within burrows, but the trends paralleled those for Shannon diversity. Yersinia was detected in four samples from one colony, marking the first time the genus has been sampled from soil on prairie dog colonies. The presence of Yersinia was a significant predictor of five bacterial families and eight microbial genera, most of which were rare taxa found in higher abundance in the presence of Yersinia, and one of which, Dictyostelium, has been proposed as an enzootic reservoir of Y. pestis. This study demonstrates that mammalian modifications to soil structure by physical alterations and by mass mortality can influence the distribution and diversity of microbial communities.

Clair SI, Bratsman S, Merritt M, Norris AJ, Carling GT, Hansen N, St. Clair SB, Abbott BW. Megafire affects stream sediment flux and dissolved organic matter reactivity, but land use dominates nutrient dynamics in semiarid watersheds

Climate change is causing larger wildfires and more extreme precipitation events in many regions. As these ecological disturbances increasingly coincide, they alter lateral fluxes of sediment, organic matter, and nutrients. Here, we report the stream chemistry response of watersheds in a semiarid region of Utah (USA) that were affected by a megafire followed by an extreme precipitation event in October 2018. We analyzed daily to hourly water samples at 10 stream locations from before the storm event until three weeks after its conclusion for suspended sediment, solute and nutrient concentrations, water isotopes, and dissolved organic matter concentration, optical properties, and reactivity. The megafire caused a ~2,000-fold increase in sediment flux and a ~6,000-fold increase in particulate carbon and nitrogen flux over the course of the storm. Unexpectedly, dissolved organic carbon (DOC) concentration was 2.1-fold higher in burned watersheds, despite the decreased organic matter from the fire. DOC from burned watersheds was 1.3-fold more biodegradable and 2.0-fold more photodegradable than in unburned watersheds based on 28-day dark and light incubations. Regardless of burn status, nutrient concentrations were higher in watersheds with greater urban and agricultural land use. Likewise, human land use had a greater effect than megafire on apparent hydrological residence time, with rapid stormwater signals in urban and agricultural areas but a gradual stormwater pulse in areas without direct human influence. These findings highlight how megafires and intense rainfall increase short-term particulate flux and alter organic matter concentration and characteristics. However, in contrast with previous research, which has largely focused on burned-unburned comparisons in pristine watersheds, we found that direct human influence exerted a primary control on nutrient status. Reducing anthropogenic nutrient sources could therefore increase socioecological resilience of surface water networks to changing wildfire regimes.

A continuous flow membrane bio-reactor releases the feedback inhibition of self-generated free organic carbon on cbb gene transcription of a typical chemoautotrophic bacterium to improve its CO2 fixation efficiency

Since the free organic carbon (FOC) generated by chemoautotrophic bacterium self has a feedback inhibition effect on its growth and carbon fixation, a continuous flow membrane bio-reactor was designed to remove extracellular FOC (EFOC) and release its inhibition effect. The promotion effect of membrane reactor on growth and carbon fixation of typical chemoautotrophic bacterium and its mechanism were studied. The accumulated apparent carbon fixation yield in membrane reactor was 3.24 times that in the control reactor. The EFOC per unit bacteria and cbb gene transcription level in membrane reactor were about 0.41 times and 11.18 times that in control reactor in late stage, respectively. Membrane reactor separated out EFOC, especially the small molecules, which facilitated the release of intracellular FOC, thereby releasing the inhibition of FOC on cbb gene transcription, thus promoting growth and carbon fixation of the typical chemoautotrophic bacterium. This study lays a foundation for enhancing carbon fixation by chemoautotrophic bacteria and expands the application field of membrane reactor.

Stream Dissolved Organic Matter in Permafrost Regions Shows Surprising Compositional Similarities but Negative Priming and Nutrient Effects

Permafrost degradation is delivering bioavailable dissolved organic matter (DOM) and inorganic nutrients to surface water networks. While these permafrost subsidies represent a small portion of total fluvial DOM and nutrient fluxes, they could influence food webs and net ecosystem carbon balance via priming or nutrient effects that destabilize background DOM. We investigated how addition of biolabile carbon (acetate) and inorganic nutrients (nitrogen and phosphorus) affected DOM decomposition with 28-day incubations. We incubated late-summer stream water from 23 locations nested in seven northern or high-altitude regions in Asia, Europe, and North America. DOM loss ranged from 3% to 52%, showing a variety of longitudinal patterns within stream networks. DOM optical properties varied widely, but DOM showed compositional similarity based on Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) analysis. Addition of acetate and nutrients decreased bulk DOM mineralization (i.e., negative priming), with more negative effects on biodegradable DOM but neutral or positive effects on stable DOM. Unexpectedly, acetate and nutrients triggered breakdown of colored DOM (CDOM), with median decreases of 1.6% in the control and 22% in the amended treatment. Additionally, the uptake of added acetate was strongly limited by nutrient availability across sites. These findings suggest that biolabile DOM and nutrients released from degrading permafrost may decrease background DOM mineralization but alter stoichiometry and light conditions in receiving waterbodies. We conclude that priming and nutrient effects are coupled in northern aquatic ecosystems and that quantifying two-way interactions between DOM properties and environmental conditions could resolve conflicting observations about the drivers of DOM in permafrost zone waterways.