Differences in thallus chemistry are related to species‐specific effects of biocrust‐forming lichens on soil nutrients and microbial communities

Tree phylogeny predicts more than litter chemical components in explaining enzyme activities in forest leaf litter decomposition

Litter decomposition is an important process in ecosystem and despite recent research elucidating the significant influence of plant phylogeny on plant-associated microbial communities, it remains uncertain whether a parallel correlation exists between plant phylogeny and the community of decomposers residing in forest litter. In this study, we conducted a controlled litterbag experiment using leaf litter from ten distinct tree species in a central subtropical forest ecosystem in a region characterized by subtropical humid monsoon climate in China. The litterbags were placed in situ using a random experimental design and were collected after 12 months of incubation. Then, the litter chemical properties, microbial community composition and activities of enzyme related to the decomposition of organic carbon (C) and nitrogen (N) were assessed. Across all ten tree species, Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were identified as the predominant bacterial classes, while the primary fungal classes were Dothideomycetes, Sordariomycetes and Eurotiomycetes. Mantel test revealed significant correlations between litter chemical component and microbial communities, as well as enzyme activities linked to N and C metabolism. However, after controlling for plant phylogenetic distance in partial Mantel test, the relationships between litter chemical component and microbial community structure and enzyme activities were not significant. Random forest and structural equation modeling indicated that plant phylogenetic distance exerted a more substantial influence than litter chemical components on microbial communities and enzyme activities associated with the decomposition of leaf litter. In summary, plant phylogenic divergence was found to be a more influential predictor of enzyme activity variations than microbial communities and litter traits, which were commonly considered reliable indicators of litter decomposition and ecosystem function, thereby highlighting the previously underestimated significance of plant phylogeny in shaping litter microbial communities and enzyme activities associated with degradation processes in forest litter.

Biocrusts increase the resistance to warming-induced increases in topsoil P pools

Ongoing global warming and alterations in rainfall patterns driven by climate change are known to have large impacts on biogeochemical cycles, particularly on drylands. In addition, the global increase in atmospheric nitrogen (N) deposition can destabilize primary productivity in terrestrial ecosystems, and phosphorus (P) may become the most limiting nutrient in many terrestrial ecosystems. However, the impacts of climate change on soil P pools in drylands remain poorly understood. Furthermore, it is unknown whether biocrusts, a major biotic component of drylands worldwide, modulate such impacts.Here we used two long-term (8-10 years) experiments conducted in Central (Aranjuez) and SE (Sorbas) Spain to test how a ~2.5°C warming, a ~30% rainfall reduction and biocrust cover affected topsoil (0-1 cm) P pools (non-occluded P, organic P, calcium bound P, occluded P and total P).Warming significantly increased most P pools-except occluded P-in Aranjuez, whereas only augmented non-occluded P in Sorbas. The rainfall reduction treatment had no effect on the soil P pools at any experimental site. Biocrusts increased most soil P pools and conferred resistance to simulated warming for major P pools at both sites, and to rainfall reduction for non-occluded and occluded P in Aranjuez. Synthesis. Our findings provide novel insights on the responses of soil P pools to warming and rainfall reduction, and highlight the importance of biocrusts as modulators of these responses in dryland ecosystems. Our results suggest that the observed negative impacts of warming on dryland biocrust communities will decrease their capacity to buffer changes in topsoil P driven by climate change.

Biological Soil Crusts as Ecosystem Engineers in Antarctic Ecosystem

Biological soil crusts (BSC) are considered as pivotal ecological elements among different ecosystems of the world. The effects of these BSC at the micro-site scale have been related to the development of diverse plant species that, otherwise, might be strongly limited by the harsh abiotic conditions found in environments with low water availability. Here, we describe for the first time the bacterial composition of BSCs found in the proximities of Admiralty Bay (Maritime Antarctica) through 16S metabarcoding. In addition, we evaluated their effect on soils (nutrient levels, enzymatic activity, and water retention), and on the fitness and performance of Colobanthus quitensis, one of the two native Antarctic vascular plants. This was achieved by comparing the photochemical performance, foliar nutrient, biomass, and reproductive investment between C. quitensis plants growing with or without the influence of BSC. Our results revealed a high diversity of prokaryotes present in these soil communities, although we found differences in terms of their abundances. We also found that the presence of BSCs is linked to a significant increase in soils' water retention, nutrient levels, and enzymatic activity when comparing with control soils (without BSCs). In the case of C. quitensis, we found that measured ecophysiological performance parameters were significantly higher on plants growing in association with BSCs. Taken together, our results suggest that BSCs in Antarctic soils are playing a key role in various biochemical processes involved in soil development, while also having a positive effect on the accompanying vascular flora. Therefore, BSCs would be effectively acting as ecosystem engineers for the terrestrial Antarctic ecosystem.

Environmental Factors Indirectly Impact the Nematode Carbon Budget of Subalpine Spruce Forests

Nematodes play a significant role in soil biogeochemical cycling. However, our understanding of their community carbon budget response for a shift in the environmental conditions of natural and planted forests is limited. Therefore, we investigated the nematode community composition, daily carbon used in production and daily carbon budget, environmental variables, and the interaction among trophic groups in the moss, litter and 0–5 cm soil layers of natural subalpine spruce forest and plantations in western Sichuan, China. The result revealed that plantations increased the total nematode daily carbon budget by approximately 52% through the herbivore channel in the 0–5 cm soil layer. The herbivorous nematodes’ daily carbon budget and production in the moss layer of plantations decreased by approximately 60% compared to natural forests. Nematode daily carbon used in production and carbon budget had a strong negative correlation with genus richness. The water content and total carbon was the most important environmental factor that affected the nematode carbon budget and production, respectively. However, the environmental factors indirectly affect the daily carbon budget of herbivore nematodes through omnivore top-down control in subalpine forest ecosystems. Our findings highlight that the planted ecosystems have a certain capacity to maintain abundance, richness, and carbon budget of soil nematode but increase the risk of herbivorous pests.

Fourteen years of continuous soil moisture records from plant and biocrust-dominated microsites

Drylands cover ~41% of the terrestrial surface. In these water-limited ecosystems, soil moisture contributes to multiple hydrological processes and is a crucial determinant of the activity and performance of above- and belowground organisms and of the ecosystem processes that rely on them. Thus, an accurate characterisation of the temporal dynamics of soil moisture is critical to improve our understanding of how dryland ecosystems function and are responding to ongoing climate change. Furthermore, it may help improve climatic forecasts and drought monitoring. Here we present the MOISCRUST dataset, a long-term (2006–2020) soil moisture dataset at a sub-daily resolution from five different microsites (vascular plants and biocrusts) in a Mediterranean semiarid dryland located in Central Spain. MOISCRUST is a unique dataset for improving our understanding on how both vascular plants and biocrusts determine soil water dynamics in drylands, and thus to better assess their hydrological impacts and responses to ongoing climate change.

Measurement(s)	soil moisture
Technology Type(s)	soil moisture sensors
Factor Type(s)	temporal interval
Sample Characteristic - Environment	semi-arid grassland
Sample Characteristic - Location	Central Spain

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.16951723

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.

Environmental and ecological factors influencing soil functionality of biologically crusted soils by different lichen species in drylands

Biocrusts are an essential soil surface cover at drylands where ecosystems are especially fragile to soil degradation processes due to climatic peculiarities. In the present work, (micro)biological and physicochemical properties indicative of soil functionality were studied in two different biocrust types dominated by Dipolschistes diacapsis and Lepraria isidiata and in underlying soil at two different depths (SL1, soil layer right below the biocrusts, and SL2, soil layer underlying SL1) at the Tabernas desert (southeast Spain). The influence of climatic factors (rainfall and temperature) and general soil properties on the (micro)biological properties were also analyzed in different environmental (climatic) conditions over a period of two years. PERMANOVA analyses showed significant statistical differences (Pseudo-F = 63.9; P (perm) = 0.001) among biocrust and soil layers. Throughout the study period, enzyme activities involved in C, N, and P cycles; microbial biomass-C; basal respiration; and several properties directly related to ecosystem productivity (total organic carbon, total nitrogen, concentration of ammonium and nitrate) were higher in both biocrust types than in the underlying soil layers, showing that biocrusts improved soil functions related to nutrient cycling. These properties progressively diminished in successive soil layers under the biocrusts (biocrusts > SL1 > SL2). Biocrusts showed greater similarity to each other and to SL1 than to SL2 in (micro)biological properties. A distance-based linear model analysis showed that total organic carbon, rainfall, pH, mineralized N-NH₄⁺, and total nitrogen were the most important variables for predicting (micro)biological soil properties in biocrusts. Different biochemical behavior between the biocrusts and successive underlying soil layers has been found in wet periods. After rainfall periods, the biocrusts showed important peaks in basal soil respiration and in enzyme activities involved in C and P cycles. Nevertheless, soil biochemical properties hardly showed any peak in SL1 and did not change in SL2 despite soil moisture being higher in the soil layers below the biocrusts. Correlation analyses corroborated the existence of different relationships between soil moisture and enzymatic activities. In biocrusts, soil moisture showed a greater number of significant positive correlations with enzymes such as β-glucosidase, invertase, and phosphomonoesterase among others, whereas in SL1 it was only correlated with cellulase and in SL2 with dehydrogenase. A change in rainfall regime, as predicted by models based on climate change in arid and semiarid zones, could affect the activity of soil enzymes in the biocrusts and underlying layers, thus aggravating the degradation of these fragile dryland ecosystems.

Soil salinity regulation of soil microbial carbon metabolic function in the Yellow River Delta, China

The ecological consequences of soil salinization, one of the major causes of soil degradation worldwide, on soil carbon (C) emissions are well known, but less is known about the related microbial C metabolic function. We conducted laboratory incubation experiments on soil samples under a salt gradient at four levels (non-saline, low, medium, and high salinity soils) from coastal saline-alkaline soil of the Yellow River Delta, China, to assess the role of soil salinity in regulating C emissions and microbial abundance. We also evaluated the associations between salt content and the read number of microbial C metabolism genes by determining the soil metagenomes. We found that soil salinity was negatively related to soil C, nitrogen (N) content, C emissions, bacterial gene copy number, and the relative abundances of Actinobacteria, Thermoleophilia, and Betaproteobacteria, but positively related to the C/N ratio and the relative abundance of Gemaproteobacteria and Halobacteria. Increases in soil salinity correlated with decreases in carbohydrate metabolism and gene abundances of glycosyl transferases and glycoside hydrolases based on the metagenomic data. In contrast, the enzyme active genes of carbohydrate esterases and auxiliary activities were positively related to soil salinity. This study provides a clear understanding of the response of soil microbial communities and their C metabolic functions to soil salinity. We offer evidence that soil salinity has significant effects on microbial communities and soil C metabolic functions, resulting in an overall negative effect on soil C emissions.

UAV RGB, thermal infrared and multispectral imagery used to investigate the control of terrain on the spatial distribution of dryland biocrust

Biocrusts (topsoil communities formed by mosses, lichens, bacteria, fungi, algae, and cyanobacteria) are a key biotic component of dryland ecosystems. Whilst climate patterns control the distribution of biocrusts in drylands worldwide, terrain and soil attributes can influence biocrust distribution at landscape scale. Multi-source unmanned aerial vehicle (UAV) imagery was used to map and study biocrust ecology in a typical dryland ecosystem in central Spain. Red, green and blue (RGB) imagery was processed using structure-from-motion techniques to map terrain attributes related to microclimate and terrain stability. Multispectral imagery was used to produce accurate maps (accuracy > 80%) of dryland ecosystem components (vegetation, bare soil and biocrust composition). Finally, thermal infrared (TIR) and multispectral imagery was used to calculate the apparent thermal inertia (ATI) of soil and to evaluate how ATI was related to soil moisture (r 2 = 0.83). The relationship between soil properties and UAV-derived variables was first evaluated at the field plot level. Then, the maps obtained were used to explore the relationship between biocrusts and terrain attributes at ecosystem level through a redundancy analysis. The most significant variables that explain biocrust distribution are: ATI (34.4% of variance, F = 130.75; p < 0.001), Elevation (25.8%, F = 97.6; p < 0.001), and potential solar incoming radiation (PSIR) (52.9%, F = 200.1; p < 0.001). Differences were found between areas dominated by lichens and mosses. Lichen-dominated biocrusts were associated with areas with high slopes and low values of ATI, with soil characterized by a higher amount of soluble salts, and lower amount of organic carbon, total phosphorus (Ptot) and total nitrogen (Ntot). Biocrust-forming mosses dominated lower and moister areas, characterized by gentler slopes and higher values of ATI with soils with higher contents of organic carbon, Ptot and Ntot. This study shows the potential to use UAVs to improve our understanding of drylands and to evaluate the control that the terrain has on biocrust distribution.

Species-specific effects of biocrust-forming lichens on soil properties under simulated climate change are driven by functional traits

Biocrusts are key drivers of ecosystem functioning in drylands, yet our understanding of how climate change will affect the chemistry of biocrust-forming species and their impacts on carbon (C) and nitrogen (N) cycling is still very limited. Using a manipulative experiment conducted with common biocrust-forming lichens with distinct morphology and chemistry (Buellia zoharyi, Diploschistes diacapsis, Psora decipiens and Squamarina lentigera), we evaluated changes in lichen total and isotopic C and N and several soil C and N variables after 50 months of simulated warming and rainfall reduction. Climate change treatments reduced δ¹³ C and the C : N ratio in B. zoharyi, and increased δ¹⁵ N in S. lentigera. Lichens had species-specific effects on soil dissolved organic N (DON), NH4+ , β-glucosidase and acid phosphatase activity regardless of climate change treatments, while these treatments changed how lichens affected several soil properties regardless of biocrust species. Changes in thallus δ¹³ C, N and C : N drove species-specific effects on dissolved organic nitrogen (DON), NH4+ , β-glucosidase and acid phosphatase activity. Our findings indicate that warmer and drier conditions will alter the chemistry of biocrust-forming lichens, affecting soil nutrient cycling, and emphasize their key role as modulators of climate change impacts in dryland soils.

Cryptogamic cover determines soil attributes and functioning in polar terrestrial ecosystems

We still lack studies that provide evidence for direct links between the development of soil surface cryptogamic communities and soil attributes and functioning. This is particularly true in areas free of potentially confounding factors such as different soil types, land uses, or anthropogenic disturbances. Despite the ecological importance of polar ecosystems and their sensitivity to climate change, we are far from understanding how their soils function and will respond to climate change-driven alterations in above- and belowground features. We used two complementary approaches (i.e. cover gradients in the forefront of retreating glaciers as well as long-time deglaciated areas with well-developed cryptogamic cover types) to evaluate the role of cryptogams driving multiple soil biotic and abiotic attributes and functioning rates in polar terrestrial ecosystems. Increases in cryptogamic cover were consistently related to increases in organic matter accumulation, soil fertility, and bacterial diversity, but also in enhanced soil functioning rates in both sampling areas. However, we also show that the ability to influence soil attributes varies among different polar cryptogamic covers, indicating that their differential ability to thrive under climate-change scenarios will largely determine the fate of polar soils in coming decades.

Effect of biocrusts on bacterial community composition at different soil depths in Mediterranean semi-arid ecosystems

This study analyzed the influence of biocrusts on the chemical properties and bacterial diversity and community composition in the underlying soils along a depth gradient (the biocrust (C1), middle (S2) and deep (S3) soil layers) in two semi-arid Mediterranean ecosystems. Organic carbon, pH, electric conductivity and calcium carbonate content were estimated by wet oxidation, potentiometrically (pHmeter), with a conductivity-meter and volumetrically with a Bernard calcimeter, respectively. Bacterial diversity and community composition were estimated by 16S rRNA gene high-throughput amplicon sequencing. Chemical properties in C1 were significantly different from the other soil layers, showing higher organic carbon content and lower pH (p < 0.05). The relative abundance of several bacterial taxa, such as Bryocella, Methylobacterium, Segitebacter and Actinomycetospora showed significant positive correlations with organic carbon (r = 0.53 to 0.75) and negative with pH (r = -0.72 to -0.84), and were also highly correlated with each other (p < 0.01), suggesting a bacterial co-occurrence pattern associated with the biocrust. On the contrary, other bacterial taxa, such as Euzebyaceae, Truepera, Alphaproteobacteria and Caldinilaceae, showed positive correlations with electrical conductivity and calcium carbonate and were also correlated with each other (p < 0.01), in a second type of co-occurrence pattern associated with bare soil. The C1 and S2 layers had several taxa in common, while S3 layers had taxa common to bare soil, suggesting that the effect of biocrusts was limited to the first centimeters of soil and progressively decreased in depth. Bacterial diversity was lower in C1 than in the underlying layers and increased progressively from biocrust to deeper soil layers. The results suggest that the diversity and composition of soil microbial communities in biologically crusted sites in Mediterranean semi-arid environments are mainly controlled by chemical properties which in turn are modified by the biocrust along a depth gradient.

Biocrusts buffer against the accumulation of soil metallic nutrients induced by warming and rainfall reduction

The availability of metallic nutrients in dryland soils, many of which are essential for the metabolism of soil organisms and vascular plants, may be altered due to climate change-driven increases in aridity. Biocrusts, soil surface communities dominated by lichens, bryophytes and cyanobacteria, are ecosystem engineers known to exert critical functions in dryland ecosystems. However, their role in regulating metallic nutrient availability under climate change is uncertain. Here, we evaluated whether well-developed biocrusts modulate metallic nutrient availability in response to 7 years of experimental warming and rainfall reduction in a Mediterranean dryland located in southeastern Spain. We found increases in the availability of K, Mg, Zn and Na under warming and rainfall exclusion. However, the presence of a well-developed biocrust cover buffered these effects, most likely because its constituents can uptake significant quantities of available metallic nutrients. Our findings suggest that biocrusts, a biotic community prevalent in drylands, exert an important role in preserving and protecting metallic nutrients in dryland soils from leaching and erosion. Therefore, we highlight the need to protect them to mitigate undesired effects of soil degradation driven by climate change in this globally expanding biome.

Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities

Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.

Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes.

Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities

Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes.IMPORTANCE Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.

Plant diversity and soil stoichiometry regulates the changes in multifunctionality during pine temperate forest secondary succession

The shift in ecosystem multifunctionality during ecosystem succession (years to decades) remains largely unexplored. In this study, we used a 120-year-old pine temperate forest chronosequence (1: 1-19 years, stage 2: 20-39 years, stage 3: 40-59 years, stage 4: 60-79 years, stage 5: 80-99 years, stage 6: 100-120 years) to evaluate the role that time plays in shaping ecosystem multifunctionality (nutrient cycling, carbon stocks, water regulation, decomposition and wood production), and found that, over the first century, ecosystem functioning gradually increased every ~50 years. Such a result was maintained for individual groups of ecosystem functions and services including nutrient cycling, carbon stocks, decomposition and wood production. Plant diversity and soil stoichiometry (C:N ratio) were the major environmental predictors for the changes in ecosystem multifunctionality during forest secondary succession. Plant diversity increased during ecosystem succession and was positively related to ecosystem multifunctionality. The soil C:N ratio decreased during ecosystem succession and was negatively related to multifunctionality. Our results suggest that increases in aboveground resource heterogeneity (higher plant diversity) and organic matter quality (lower soil C:N ratios) could help explain the increases in multifunctionality over a century of forest development. Our work illustrates the importance of time in shaping multifunctionality during the first century of ecosystem succession, and further provide important insights for the management of temperate forest ecosystems.

Sediment pH, not the bacterial diversity, determines Escherichia coli O157:H7 survival in estuarine sediments

Shiga toxin-producing Escherichia coli (E. coli) O157:H7 is recognized as a hazardous microorganism in the environment. Its longer survival might contribute to higher contamination risk. In this study, E. coli O157:H7 survival in estuarine sediments collected from south Hangzhou Bay was investigated. The survival time of E. coli O157:H7 in estuarine sediments increased with the distance to the water-land junction. Sediment pH was the most important factor in regulating E. coli O157:H7 survival in estuarine sediments. In addition, sediment nutrients and texture also played significant roles in the survival of E. coli O157:H7 in the sediments. On the other hand, bacterial diversity as determined by the alpha-diversity index had no significant effect on E. coli O157:H7 survival. However, specific families of bacteria were closely associated with E. coli O157:H7 survival in the sediments. Remarkably, some potential bacterial groups, e.g., the Desulfobacteraceae, Desulfobulbaceae and Desulfarculaceae families, which are mainly involved in the sulfur cycle, showed significant negative correlation with the E. coli O157:H7 survival in the sediments. On the whole, abiotic factors showed greater effects on E. coli O157:H7 survival in the test sediments than the bacterial community. Our findings provide a comprehensive understanding of E. coli O157:H7 survival and regulatory factors in estuarine sediments, establishing foundation for the prevention of pathogen contamination.

Global ecological predictors of the soil priming effect

Identifying the global drivers of soil priming is essential to understanding C cycling in terrestrial ecosystems. We conducted a survey of soils across 86 globally-distributed locations, spanning a wide range of climates, biotic communities, and soil conditions, and evaluated the apparent soil priming effect using ¹³C-glucose labeling. Here we show that the magnitude of the positive apparent priming effect (increase in CO₂ release through accelerated microbial biomass turnover) was negatively associated with SOC content and microbial respiration rates. Our statistical modeling suggests that apparent priming effects tend to be negative in more mesic sites associated with higher SOC contents. In contrast, a single-input of labile C causes positive apparent priming effects in more arid locations with low SOC contents. Our results provide solid evidence that SOC content plays a critical role in regulating apparent priming effects, with important implications for the improvement of C cycling models under global change scenarios.

The global ecological predictors of soil priming remain unclear. Here the authors conducted a global survey of soils from 86 global locations using an isotopic approach and find that in more mesic sites with high SOC concentrations, soil priming effects are more likely to be negative.

A few Ascomycota taxa dominate soil fungal communities worldwide

Despite having key functions in terrestrial ecosystems, information on the dominant soil fungi and their ecological preferences at the global scale is lacking. To fill this knowledge gap, we surveyed 235 soils from across the globe. Our findings indicate that 83 phylotypes (<0.1% of the retrieved fungi), mostly belonging to wind dispersed, generalist Ascomycota, dominate soils globally. We identify patterns and ecological drivers of dominant soil fungal taxa occurrence, and present a map of their distribution in soils worldwide. Whole-genome comparisons with less dominant, generalist fungi point at a significantly higher number of genes related to stress-tolerance and resource uptake in the dominant fungi, suggesting that they might be better in colonising a wide range of environments. Our findings constitute a major advance in our understanding of the ecology of fungi, and have implications for the development of strategies to preserve them and the ecosystem functions they provide.

Soil fungi play essential roles in ecosystems worldwide. Here, the authors sequence and analyze 235 soil samples collected from across the globe, and identify dominant fungal taxa and their associated environmental attributes.

Australian dryland soils are acidic and nutrient-depleted, and have unique microbial communities compared with other drylands

AIM

To compare Australian dryland soils with dryland soils globally.

LOCATION

Australian and global drylands.

METHODS

We used data from standardized surveys of soil properties (C:N:P content and stoichiometry, and pH), and microbes (diversity, composition and correlation networks) from Australian and global drylands, which occupy three-quarters of the Australian land mass and are the largest biome on Earth.

RESULTS

We found that Australian dryland soils were different, exhibiting characteristics of ancient weathered soils. They had lower pH, total and available P, and total N, and greater C:N and C:P ratios than global dryland soils. Australian soils had distinctive microbial community composition and diversity, with more Proteobacteria and fewer Basidiomycota than global dryland soils, and promoted the abundance of specific microbial phylotypes including pathogens, mycorrhizae and saprobes.

MAIN CONCLUSIONS

Australian dryland soils are clearly different from dryland soils elsewhere. These differences need to be considered when managing dryland soils to avoid unreasonable expectations about plant productivity and carbon stocks, or when predicting likely changes in ecosystem processes resulting from global environmental change.

Carbon Consumption Patterns of Microbial Communities Associated with Peltigera Lichens from a Chilean Temperate Forest

Lichens are a symbiotic association between a fungus and a green alga or a cyanobacterium, or both. They can grow in practically any terrestrial environment and play crucial roles in ecosystems, such as assisting in soil formation and degrading soil organic matter. In their thalli, they can host a wide diversity of non-photoautotrophic microorganisms, including bacteria, which play important functions and are considered key components of the lichens. In this work, using the BioLog^® EcoPlate system, we studied the consumption kinetics of different carbon-sources by microbial communities associated with the thallus and the substrate of Peltigera lichens growing in a Chilean temperate rain forest dominated by Nothofagus pumilio. Based on the similarity of the consumption of 31 carbon-sources, three groups were formed. Among them, one group clustered the microbial metabolic profiles of almost all the substrates from one of the sampling sites, which exhibited the highest levels of consumption of the carbon-sources, and another group gathered the microbial metabolic profiles from the lichen thalli with the most abundant mycobiont haplotypes. These results suggest that the lichen thallus has a higher impact on the metabolism of its microbiome than on the microbial community of its substrate, with the latter being more diverse in terms of the metabolized sources and whose activity level is probably related to the availability of soil nutrients. However, although significant differences were detected in the microbial consumption of several carbon-sources when comparing the lichen thallus and the underlying substrate, d-mannitol, l-asparagine, and l-serine were intensively metabolized by both communities, suggesting that they share some microbial groups. Likewise, some communities showed high consumption of 2-hydroxybenzoic acid, d-galacturonic acid, and itaconic acid; these could serve as suitable sources of microorganisms as bioresources of novel bioactive compounds with biotechnological applications.

Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China

BACKGROUND

The ecological consequences of mercury (Hg) pollution-one of the major pollutants worldwide-on microbial taxonomic and functional attributes remain poorly understood and largely unexplored. Using soils from two typical Hg-impacted regions across China, here, we evaluated the role of Hg pollution in regulating bacterial abundance, diversity, and co-occurrence network. We also investigated the associations between Hg contents and the relative abundance of microbial functional genes by analyzing the soil metagenomes from a subset of those sites.

RESULTS

We found that soil Hg largely influenced the taxonomic and functional attributes of microbial communities in the two studied regions. In general, Hg pollution was negatively related to bacterial abundance, but positively related to the diversity of bacteria in two separate regions. We also found some consistent associations between soil Hg contents and the community composition of bacteria. For example, soil total Hg content was positively related to the relative abundance of Firmicutes and Bacteroidetes in both paddy and upland soils. In contrast, the methylmercury (MeHg) concentration was negatively correlated to the relative abundance of Nitrospirae in the two types of soils. Increases in soil Hg pollution correlated with drastic changes in the relative abundance of ecological clusters within the co-occurrence network of bacterial communities for the two regions. Using metagenomic data, we were also able to detect the effect of Hg pollution on multiple functional genes relevant to key soil processes such as element cycles and Hg transformations (e.g., methylation and reduction).

CONCLUSIONS

Together, our study provides solid evidence that Hg pollution has predictable and significant effects on multiple taxonomic and functional attributes including bacterial abundance, diversity, and the relative abundance of ecological clusters and functional genes. Our results suggest an increase in soil Hg pollution linked to human activities will lead to predictable shifts in the taxonomic and functional attributes in the Hg-impacted areas, with potential implications for sustainable management of agricultural ecosystems and elsewhere.

Simulated climate change affects how biocrusts modulate water gains and desiccation dynamics after rainfall events

Soil surface communities dominated by mosses, lichens and cyanobacteria (biocrusts) are common between vegetation patches in drylands worldwide, and are known to affect soil wetting and drying after rainfall events. While ongoing climate change is already warming and changing rainfall patterns of drylands in many regions, little is known on how these changes may affect the hydrological behaviour of biocrust-covered soils. We used eight years of continuous soil moisture and rainfall data from a climate change experiment in central Spain to explore how biocrusts modify soil water gains and losses after rainfall events under simulated changes in temperature (2.5°C warming) and rainfall (33% reduction). Both rainfall amount and biocrust cover increased soil water gains after rainfall events, whereas experimental warming, rainfall intensity and initial soil moisture decreased them. Initial moisture, maximum temperature and biocrust cover, by means of enhancing potential evapotranspiration or by soil darkening, increased the drying rates and enhanced the exponential behaviour of the drying events. Meanwhile, warming reduced their exponential behaviour. The effects of climate change treatments on soil water gains and losses changed through time, with important differences between the first two years of the experiment and five years after its setup. These effects were mainly driven by the important reductions in biocrust cover and diversity observed under warming. Our results highlight the importance of long-term studies to understand soil moisture responses to ongoing climate change in drylands.

Identity of plant, lichen and moss species connects with microbial abundance and soil functioning in Maritime Antarctica

BACKGROUND AND AIMS

We lack studies evaluating how the identity of plant, lichen and moss species relates to microbial abundance and soil functioning on Antarctica. If species identity is associated with soil functioning, distributional changes of key species, linked to climate change, could significantly affect Antarctic soil functioning.

METHODS

We evaluated how the identity of six Antarctic plant, lichen and moss species relates to a range of soil attributes (C, N and P cycling), microbial abundance and structure in Livingston Island, Maritime Antarctica. We used an effect size metric to predict the association between species (vs. bare soil) and the measured soil attributes.

RESULTS

We observed species-specific effects of the plant and biocrust species on soil attributes and microbial abundance. Phenols, phosphatase and β-D-cellobiosidase activities were the most important attributes characterizing the observed patterns. We found that the evaluated species positively correlated with soil nutrient availability and microbial abundance vs. bare soil.

CONCLUSIONS

We provide evidence, from a comparative study, that plant and biocrust identity is associated with different levels of soil functioning and microbial abundance in Maritime Antarctica. Our results suggest that changes in the spatial distribution of these species linked to climate change could potentially entail changes in the functioning of Antarctic terrestrial ecosystems.

How lichens impact on terrestrial community and ecosystem properties

Lichens occur in most terrestrial ecosystems; they are often present as minor contributors, but in some forests, drylands and tundras they can make up most of the ground layer biomass. As such, lichens dominate approximately 8% of the Earth's land surface. Despite their potential importance in driving ecosystem biogeochemistry, the influence of lichens on community processes and ecosystem functioning have attracted relatively little attention. Here, we review the role of lichens in terrestrial ecosystems and draw attention to the important, but often overlooked role of lichens as determinants of ecological processes. We start by assessing characteristics that vary among lichens and that may be important in determining their ecological role; these include their growth form, the types of photobionts that they contain, their key functional traits, their water-holding capacity, their colour, and the levels of secondary compounds in their thalli. We then assess how these differences among lichens influence their impacts on ecosystem and community processes. As such, we consider the consequences of these differences for determining the impacts of lichens on ecosystem nutrient inputs and fluxes, on the loss of mass and nutrients during lichen thallus decomposition, and on the role of lichenivorous invertebrates in moderating decomposition. We then consider how differences among lichens impact on their interactions with consumer organisms that utilize lichen thalli, and that range in size from microfauna (for which the primary role of lichens is habitat provision) to large mammals (for which lichens are primarily a food source). We then address how differences among lichens impact on plants, through for example increasing nutrient inputs and availability during primary succession, and serving as a filter for plant seedling establishment. Finally we identify areas in need of further work for better understanding the role of lichens in terrestrial ecosystems. These include understanding how the high intraspecific trait variation that characterizes many lichens impacts on community assembly processes and ecosystem functioning, how multiple species mixtures of lichens affect the key community- and ecosystem-level processes that they drive, the extent to which lichens in early succession influence vascular plant succession and ecosystem development in the longer term, and how global change drivers may impact on ecosystem functioning through altering the functional composition of lichen communities.

Intrinsic factors of Peltigera lichens influence the structure of the associated soil bacterial microbiota

Definition of lichens has evolved from bi(tri)partite associations to multi-species symbioses, where bacteria would play essential roles. Besides, although soil bacterial communities are known to be affected by edaphic factors, when lichens grow upon them these could become less preponderant. We hypothesized that the structure of both the lichen microbiota and the microbiota in the soil underneath lichens is shaped by lichen intrinsic and extrinsic factors. In this work, intrinsic factors corresponded to mycobiont and cyanobiont identities of Peltigera lichens, metabolite diversity and phenoloxidase activity and extrinsic factors involved the site of the forest where lichens grow. Likewise, the genetic and metabolic structure of the lichen and soil bacterial communities were analyzed by fingerprinting. Among the results, metabolite diversity was inversely related to the genetic structure of bacterial communities of lichens and soils, highlighting the far-reaching effect of these substances; while phenoloxidase activity was inversely related to the metabolic structure only of the lichen bacterial microbiota, presuming a more limited effect of the products of these enzymes. Soil bacterial microbiota was different depending on the site and, strikingly, according to the cyanobiont present in the lichen over them, which could indicate an influence of the photobiont metabolism on the availability of soil nutrients.

Microbial regulation of the soil carbon cycle: evidence from gene-enzyme relationships

A lack of empirical evidence for the microbial regulation of ecosystem processes, including carbon (C) degradation, hinders our ability to develop a framework to directly incorporate the genetic composition of microbial communities in the enzyme-driven Earth system models. Herein we evaluated the linkage between microbial functional genes and extracellular enzyme activity in soil samples collected across three geographical regions of Australia. We found a strong relationship between different functional genes and their corresponding enzyme activities. This relationship was maintained after considering microbial community structure, total C and soil pH using structural equation modelling. Results showed that the variations in the activity of enzymes involved in C degradation were predicted by the functional gene abundance of the soil microbial community (R²>0.90 in all cases). Our findings provide a strong framework for improved predictions on soil C dynamics that could be achieved by adopting a gene-centric approach incorporating the abundance of functional genes into process models.

Microsite Differentiation Drives the Abundance of Soil Ammonia Oxidizing Bacteria along Aridity Gradients

Soil ammonia oxidizing bacteria (AOB) and archaea (AOA) are responsible for nitrification in terrestrial ecosystems, and play important roles in ecosystem functioning by modulating the rates of N losses to ground water and the atmosphere. Vascular plants have been shown to modulate the abundance of AOA and AOB in drylands, the largest biome on Earth. Like plants, biotic and abiotic features such as insect nests and biological soil crusts (biocrusts) have unique biogeochemical attributes (e.g., nutrient availability) that may modify the local abundance of AOA and AOB. However, little is known about how these biotic and abiotic features and their interactions modulate the abundance of AOA and AOB in drylands. Here, we evaluate the abundance of amoA genes from AOB and AOA within six microsites commonly found in drylands (open areas, biocrusts, ant nests, grasses, nitrogen-fixing shrubs, and trees) at 21 sites from eastern Australia, including arid and mesic ecosystems that are threatened by predicted increases in aridity. Our results from structural equation modeling suggest that soil microsite differentiation alters the abundance of AOB (but not AOA) in both arid and mesic ecosystems. While the abundance of AOA sharply increased with increasing aridity in all microsites, the response of AOB abundance was microsite-dependent, with increases (nitrogen-fixing shrubs, ant nests), decreases (open areas) or no changes (grasses, biocrusts, trees) in abundance with increasing aridity. Microsites supporting the highest abundance of AOB were trees, nitrogen-fixing shrubs, and ant nests. These results are linked to particular soil characteristics (e.g., total carbon and ammonium) under these microsites. Our findings advance our understanding of key drivers of functionally important microbial communities and N availability in highly heterogeneous ecosystems such as drylands, which may be obscured when different soil microsites are not explicitly considered.

Biocrust-forming mosses mitigate the negative impacts of increasing aridity on ecosystem multifunctionality in drylands

The increase in aridity predicted with climate change will have a negative impact on the multiple functions and services (multifunctionality) provided by dryland ecosystems worldwide. In these ecosystems, soil communities dominated by mosses, lichens and cyanobacteria (biocrusts) play a key role in supporting multifunctionality. However, whether biocrusts can buffer the negative impacts of aridity on important biogeochemical processes controlling carbon (C), nitrogen (N), and phosphorus (P) pools and fluxes remains largely unknown. Here, we conducted an empirical study, using samples from three continents (North America, Europe and Australia), to evaluate how the increase in aridity predicted by climate change will alter the capacity of biocrust-forming mosses to modulate multiple ecosystem processes related to C, N and P cycles. Compared with soil surfaces lacking biocrusts, biocrust-forming mosses enhanced multiple functions related to C, N and P cycling and storage in semiarid and arid, but not in humid and dry-subhumid, environments. Most importantly, we found that the relative positive effects of biocrust-forming mosses on multifunctionality compared with bare soil increased with increasing aridity. These results were mediated by plant cover and the positive effects exerted by biocrust-forming mosses on the abundance of soil bacteria and fungi. Our findings provide strong evidence that the maintenance of biocrusts is crucial to buffer negative effects of climate change on multifunctionality in global drylands.