Soil Biogeochemical Cycling Research Articles

Active tailings disturb the surrounding vegetation soil fungal community: Diversity, assembly process and co-occurrence patterns

Soil fungi play an important role in the soil biogeochemical cycle and are important biological indicators for the ecological remediation of mine tailings contaminated sites, therefore understanding the characteristics of soil fungal communities is a key aspect of pollution remediation. However, the influence of biological factors on the characteristics of fungal community diversity; assembly mechanisms and co-occurrence patterns of fungal community along environmental gradients around tailings are not well understood. In this study, soil samples from forest, agriculture and grass around tailings were collected to reveal the assembly mechanisms and co-occurrence patterns of soil fungal community and to quantify the contribution of abiotic and biotic factors to fungal diversity. The results suggest that vegetation types and Cu concentration together drive the distribution of fungal diversity. We found that Exophiala has potential as a biomarker species indicative of restoration progress. Increased environmental stress accelerates the process of changing fungal community assemblages from stochastic to deterministic, while also allowing fungal communities tend to resist tailings-induced environmental stresses through species coexistence. Together, this study provides new insights into the influence of biological factors on fungal community diversity, as well as revealing mechanisms of fungal community assembly and co-occurrence patterns, which are important for understanding the maintenance mechanisms of fungal community diversity and ecological remediation of tailings-contaminated soils.

Soil Fungal Diversity and Functionality Changes Associated with Multispecies Restoration of Pinus massoniana Plantation in Subtropical China

Soil fungi play a critical role in the carbon and nutrient cycling of forest ecosystems. Identifying the composition of soil fungi in response to the broadleaf restoration of Pinus massoniana plantation is essential for exploring the mechanistic linkages between tree species and ecological processes, but remains unexplored. We compared the shifts in soil fungal diversity and guilds by high–throughput sequencing between two P. massoniana plantations at different stand ages, two modes of restoration with broadleaf trees, and a secondary forest in subtropical China. We found that soil fungal taxonomic and functional compositions significantly differed among forests. The highest Chao 1, Shannon, and phylogenetic diversity indices were consistently observed in the two P. massoniana monocultures, followed by the two modes of broadleaf mixing, and the secondary forests. Fungal communities transitioned from Ascomycota-dominated at P. massoniana plantations to Basidiomycota-dominated at other forests in the topsoil. Furthermore, saprotrophs and symbiotrophs were favoured in plantations and secondary forests, respectively. Soil pH exerted the most significant effect on the relative abundance of Ascomycota and Rozellomycota, as well as the saprotrophs. Moreover, the dominant phyla of Ascomycota, Mucoromycota, and Rozellomycota were negatively related to soil microbial biomass nitrogen, ammonium nitrogen, and total nitrogen contents; however, Mortierellomycota benefited from the elevated soil ammonium nitrogen content. On the other hand, soil nitrate nitrogen and available phosphorus contents strongly and negatively influenced the ectomycorrhizal fungi, while the other fungal guilds were mainly affected by soil pH. Our findings guide an evaluation of the consequences of forest restoration and contribute to an improved understanding of the mechanisms behind soil biogeochemical cycling in subtropical forest ecosystems.

Metatranscriptomics reveals contrasting effects of elevation on the activity of bacteria and bacterial viruses in soil.

Soil microbial diversity affects ecosystem functioning and global biogeochemical cycles. Soil bacterial communities catalyse a diversity of biogeochemical reactions and have thus sparked considerable scientific interest. One driver of bacterial community dynamics in natural ecosystems has so far been largely neglected: the predator-prey interactions between bacterial viruses (bacteriophages) and bacteria. To generate ground level knowledge on environmental drivers of these particular predator-prey dynamics, we propose an activity-based ecological framework to simultaneous capture community dynamics of bacteria and bacteriophages in soils. An ecological framework and specifically the analyses of community dynamics across latitudinal and elevational gradients have been widely used in ecology to understand community-wide responses of innumerable taxa to environmental change, in particular to climate. Here, we tested the hypothesis that the activity of bacteria and bacteriophages codeclines across an elevational gradient. We used metatranscriptomics to investigate bacterial and bacteriophage activity patterns at five sites across 400 elevational metres in the Swiss Alps in 2015 and 2017. We found that metabolic activity (transcription levels) of bacteria declined significantly with increasing elevation, but activity of bacteriophages did not. We showed that bacteriophages are consistently active in soil along the entire gradient, making bacteriophage activity patterns divergent from that of their putative bacterial prey. Future efforts will be necessary to link the environment-activity relationship to predator-prey dynamics, and to understand the magnitude of viral contributions to carbon, nitrogen and phosphorus cycling when infection causes bacterial cell death, a process that may represent an overlooked component of soil biogeochemical cycles.

Shifting soil nutrient stoichiometry with soil of variable rock fragment contents and different vegetation types

Soil nutrient contents and stoichiometric ratios are determinants for soil biogeochemical cycling and functions. Variable rock fragment contents (RFC) may shape the soil nutrient status and availability in mountain ecosystems. We need to better understand how and why soil nutrients and stoichiometry shift across the RFC gradients. To investigate patterns of soil nutrient stoichiometry and underlying mechanisms in rocky soils, we conducted a field experiment involving four RFCs gradients (0%, 25%, 50% and 75%, V/V) and five vegetation treatments (four indigenous species, Artemisia vestita, Bauhinia brachycarpa, Cotinus szechuanensis and Sophora davidii, plus a non-planted treatment). Soil total carbon (C), total nitrogen (N), total phosphorus (P) and their molar ratios were measured. The contents of soil C, N and P, and C:N, C:P and N:P decreased with increasing RFC in all treatments, despite their trends were inconsistent in certain soil layers. The averages of soil N content significantly increased by 13.8% and 14.8% in C. szechuanensis and S. davidii, respectively. A. vestita and B. brachycarpa had higher soil C:N than C. szechuanensis and S. davidii. Soil nutrients and stoichiometry were positively related to soil water content (SWC) and soil capillary porosity, and negatively to bulk density and soil non-capillary porosity in all vegetation treatments, but varying relationships with biomass of plant components. These results demonstrated negative effect of RFC and discrepant effects of the plants on soil nutrients and stoichiometry. Soil structure, SWC and vegetation were the main drivers of variations in soil nutrient stoichiometry. We further concluded that soil nutrient stoichiometry in rocky soils is shaped by two influencing paths; effects of RFC on soil physical properties (SWC and soil structure) and effects of different vegetations. Our findings advance knowledge and mechanisms of soil nutrient stoichiometry in rocky soils and provide theoretical support for improving and restoring nutrient status in stony regions.

Corner Flows Induced by Surfactant-Producing Bacteria Bacillus subtilis and Pseudomonas fluorescens.

ABSTRACTA mechanistic understanding of bacterial spreading in soil, which has both air and water in angular pore spaces, is critical to control pathogenic contamination of soil and to design bioremediation projects. A recent study (J. Q. Yang, J. E. Sanfilippo, N. Abbasi, Z. Gitai, et al., Proc Natl Acad Sci U S A 118:e2111060118, 2021, https://doi.org/10.1073/pnas.2111060118) shows that Pseudomonas aeruginosa can self-generate flows along sharp corners by producing rhamnolipids, a type of biosurfactants that change the hydrophobicity of solid surfaces. We hypothesize that other types of biosurfactants and biosurfactant-producing bacteria can also generate corner flows. Here, we first demonstrate that rhamnolipids and surfactin, biosurfactants with different chemical structures, can generate corner flows. We identify the critical concentrations of these two biosurfactants to generate corner flow. Second, we demonstrate that two common soil bacteria, Pseudomonas fluorescens and Bacillus subtilis (which produce rhamnolipids and surfactin, respectively), can generate corner flows along sharp corners at the speed of several millimeters per hour. We further show that a surfactin-deficient mutant of B. subtilis cannot generate corner flow. Third, we show that, similar to the finding for P. aeruginosa, the critical corner angle for P. fluorescens and B. subtilis to generate corner flows can be predicted from classic corner flow theories. Finally, we show that the height of corner flows is limited by the roundness of corners. Our results suggest that biosurfactant-induced corner flows are prevalent in soil and should be considered in the modeling and prediction of bacterial spreading in soil. The critical biosurfactant concentrations we identify and the mathematical models we propose will provide a theoretical foundation for future predictions of bacterial spreading in soil.IMPORTANCE The spread of bacteria in soil is critical in soil biogeochemical cycles, soil and groundwater contamination, and the efficiency of soil-based bioremediation projects. However, the mechanistic understanding of bacterial spreading in soil remains incomplete due to a lack of direct observations. Here, we simulate confined spaces of hydrocarbon-covered soil using a transparent material with similar hydrophobicity and visualize the spread of two common soil bacteria, Pseudomonas fluorescens and Bacillus subtilis. We show that both bacteria can generate corner flows at the velocity of several millimeters per hour by producing biosurfactants, soap-like chemicals. We provide quantitative equations to predict the critical corner angle for bacterial corner flow and the maximum distance of the corner spreading. We anticipate that bacterial corner flow is prevalent because biosurfactant-producing bacteria and angular pores are common in soil. Our results will help improve predictions of bacterial spreading in soil and facilitate the design of soil-related bioremediation projects.

Decoupled cycling of carbon, nitrogen, and phosphorus in a grassland soil along a hillslope mediated by clay and soil moisture

Grasslands extend across a variety of topographies including non-flat hilly areas with varied soil texture and moisture that can mediate soil biogeochemical cycling of carbon (C), nitrogen (N) and phosphorus (P). In this study we examined soil organic C, total N and P pools (both inorganic and organic), as well as gross N mineralisation (GNM, as a measure of microbial activity and N dynamics) and microbial C, N and P in winter and spring along a grassland hillslope. Our results showed that variation in soil clay and associated soil moisture were the most important mediators affecting C and N dynamics along the grassland elevational gradient. Total organic C pools were highest where the clay content was highest, likely because of the sorption capacity of clay stabilising organic matter against microbial decomposition. Likewise, the variation in soil organic N pools along the hillslope was mostly controlled by clay and soil moisture effects on microbial stabilisation of organic N. Furthermore, microbial C, N and GNM increased with increased soil moisture, suggesting that microbial activity was limited by soil moisture. In contrast, soil P pools were not related to clay and soil moisture, while soil organic P was decoupled from soil organic C and N pools along the hillslope. Possibly, differences in microbial stabilisation and mineralisation pathways (oxidation for C and N, hydrolysis for P), microbial homeostatic regulation of C, N and P, and P fixation resulted in a decoupling of P from C and N cycling in this grassland. We conclude that variation in clay and associated soil moisture along grassland hillslopes can have important but non-unidirectional effects on soil C, N and P cycling.

Disentangling effects of upslope runoff and sediment on soil nutrients on the hilly slopes of the Loess Plateau, China

Upslope runoff and sediment critically influence soil erosion, while their impact on the subsequent downslope nutrient distribution has not been examined, consequently hindering the exact assessment of the effects of erosion on soil biogeochemical cycles. Herein we selected two groups of wide and narrow slopes on the middle Loess Plateau, with each slope group including slopes with and without upslope runoff and sediment. For each slope, we collected soil samples from topsoil along the slope at different distances from the upper slope to the lower slope, and collected samples from depths of 0–60 cm at the upper, middle and lower positions of the slope. The contents of soil organic matter and nutrients were analysed. The purpose of this study was to disentangle the effects of upslope runoff and sediment on spatial distribution of soil nutrients on slopes of different widths. We showed that compared with slopes without upslope runoff and sediment, upslope runoff and sediment increased the content of most nutrients in topsoil on the wide slope, but had a contrasting effect on the narrow slope. Upslope runoff and sediment reduced the random spatial heterogeneity of soil nutrients on both the wide and narrow slopes, with greater effects observed on the narrow slope. The influence of upslope runoff and sediment on the profile distribution of soil nutrients varied with slope position and slope width, and was nutrient type-dependent. These results indicated that slope topographical conditions interact with upslope runoff and sediment in influencing vertical and horizontal patterns of soil nutrients on slopes.

Snowbed communities and soil C and N dynamics during a four-year investigation in the NW-Italian Alps

ABSTRACT The snowbed habitats represent a relevant component of the alpine tundra biome, developing in areas characterized by a long-lasting snow cover. Such areas are particularly sensitive to climate changes, because small variations in air temperature, rain, and snowfall may considerably affect the pedoclimate and plant phenology, which control the soil C and N cycling. Therefore, it is fundamental to identify the most sensitive abiotic and biotic variables affecting soil nutrient cycling. This work was performed at seven permanent snowbed sites belonging to Salicetum herbaceae vegetation community in the northwestern Italian Alps, at elevations between 2,686 and 2,840 m.a.s.l. During a four-year study, we investigated climate, pedoclimate, floristic composition, phenology, and soil C and N dynamics. We found that lower soil water content and earlier melt-out day decreased soil N-NH4 +, N-NO3 −, dissolved organic carbon (DOC), dissolved organic nitrogen (DON), total dissolved nitrogen (TDN), microbial nitrogen (Nmicr), microbial carbon (Cmicr), and C:Nmicr ratio. The progression of the phenological stages of Salix herbacea reduced soil N-NH4 + and increased DOC. Our results showed that the snow melt-out day, soil temperature, soil water content, and plant phenological stages were the most important factors affecting soil biogeochemical cycles, and they should be taken into account when assessing the effects of climate change in alpine tundra ecosystems, in the framework of long-term ecological research.

Impacts of deficit irrigation and organic amendments on soil microbial populations and yield of processing tomatoes

Altered precipitation patterns and increased water demands from urban, industrial, and environmental needs often reduce the volume of irrigation water available for agriculture. Strategies that reduce irrigation water inputs, e.g., deficit irrigation (DI), need further evaluation to determine potential impacts on yield and soil microbial communities driving critical soil biogeochemical cycles. Whether soil organic amendments can stabilize DI effects on yield and microbial communities remains unknown. Processing tomato beds were established in a full factorial experimental design of soils unamended or amended with a one-time application—four to five years before sampling—of either biochar or biochar with compost and three irrigation regimes: full (100 % of plant water demand), or DI treatments at 75 % or 50 % of full irrigation. We profiled soil bacterial and archaeal community compositions for two growing seasons and determined soil C and N metabolic potentials and biomass of microbial groups using high throughput sequencing of 16S rRNA genes and phospholipid fatty acid analysis. We tested the discrete and interactive effects of DI and soil amendments on soil chemical and biological properties, and crop yield. DI had stronger effects on the bacterial and archaeal community composition than soil organic amendments. However, 75 % DI did not strongly affect bacterial and archaeal community composition or the total and individual biomass of microbial groups, but it increased irrigation water productivity of processing tomatoes. Although soil amendments did not stabilize the compositional shifts induced by DI, their recalcitrant C still had residual effects on the bacterial and archaeal community composition years after their incorporation. Furthermore, soil moisture correlated with bacterial and archaeal community's C and N metabolic potentials, likely augmenting the amendments' C and N residence time in DI soils. Our results provide insight into water-saving mechanisms that could increase profit margins in water-scarce years without affecting microbial populations that support plant growth and productivity.

Lignin and fungal abundance modify manganese effects on soil organic carbon persistence at the continental scale

Manganese (Mn) may play an outsized role in soil biogeochemical cycles relative to its abundance. The role of Mn-facilitated oxidation of biomacromolecules during litter decomposition is well-established, but the balance between Mn-promoted soil organic carbon (SOC) oxidation and long-term SOC protection in mineral soils is unknown, especially in subsoils. In this study, we used soils collected across the US National Ecological Observatory Network (NEON) to assess the distribution of Mn and relationships between Mn abundance and SOC concentration, potential mineralization, and persistence at a continental spatial scale. Total reducible Mn was not spatially correlated to site moisture (Spearman’s Rho = 0.24), highlighting that Mn abundance may influence SOC cycling independently from other moisture-driven soil chemical properties (e.g., reactive iron and aluminum). However, Mn effects on SOC cycling depended on depth, soil, or site-level properties. In particular, fungal:bacterial biomass ratio, proportion of SOC in the free light fraction, lignin abundance, and/or proportion of undegraded organic matter mediated the effect of Mn on SOC cycling metrics. For example, the effect of Mn on SOC concentration in subsoils shifted from positive (approximately +270 % relative to mean subsoil SOC) to negative (−125 %) with increasing fungal:bacterial ratio. We propose that convergence of high Mn, lignin-rich substrates, and fungal:bacterial ratio amplifies lignin mineralization in surface soils, but does not result in higher net SOC turnover due to fungal biomass stabilization. In contrast, we suggest that Mn abundance promotes smaller, but more persistent SOC stocks in subsoils by accelerating SOC transformation from particulate to microbial biomass pools.

Changes in litter input exert divergent effects on the soil microbial community and function in stands of different densities

Soil microbial communities influence soil biogeochemical cycling by affecting the production of extracellular enzymes and the release of carbon dioxide. Changes in litter input or stand density due to thinning can affect soil microbial communities and their function by altering soil biochemical properties. However, it is unclear how or to what extent different amounts of litter input affect soil microbial communities and their function in forest stands with different densities. Therefore, we simulated litter removal, 50 % litter reduction, normal litter input, and double litter increase under field conditions by applying different amounts of litter to soils with different stand densities in the laboratory. We then measured soil biochemical properties, microbial communities, enzyme activity, and respiration rate.Our results revealed that the responses of soil dissolved organic carbon and total nitrogen to litter input were more pronounced in the high-density forest stand with poor soil than in the low-density forest stand with nutrient-rich soil, which was mainly reflected in that the addition of litter significantly decreased the concentration of dissolved organic carbon while increasing the content of total nitrogen in the soil of the high-density forest stand. In comparison to the soil carbon component, the nitrogen component of the soil was more affected by stand density. The responses of soil fungal and bacterial communities to leaf litter treatment varied with stand density, as reflected primarily in changes in the relative abundances of Ascomycota, unclassified_K_fungi, and Proteobacteria, and changes in the relative abundances of their functional groups (ectomycorrhizal fungi, saprophytic fungi, pathogens, parasites, and bacteria involved in the nitrogen cycle). Soil fungal community responses to changes in litter input are more sensitive in the high-density forest with nutrient-poor soil than in the low-density forest stand. Furthermore, litter input inhibited the activities of soil β-glucuronidase, N-acetyl-β-d-glucosaminidase, and acid phosphatase more strongly in the low-density forest stand. Litter manipulation primarily affected enzymatic activity in the high-density forest stand by changing the diversity and composition of the soil fungal community. However, in the low-density forest stand, litter treatment affected soil enzyme activity, primarily through changes in soil bacterial and fungal community composition, as well as soil respiration through changes in bacterial richness (Chao 1) and community composition.We conclude that how the change in litter input impacts the soil microbial community and its function, or the magnitude of the effects, is largely dependent on soil quality. Relationships among soil variables, microbial communities, and function differ between stand densities. Our study contributes to an enhanced understanding of the impact of changes in litter input due to climate change or anthropogenic activities on soil biogeochemical cycles and can also guide rationally formulating forest management approaches to improve microbial function under climate change.

Context dependence in a tropical forest: Repeated disturbance reduces soil nitrate response but increases phosphate

AbstractHurricanes and other extreme events are increasing in many regions, yet their long‐term impacts on ecosystem function are uncertain. In forested ecosystems, soil solution chemistry provides an important tool to assess the impacts of disturbance on nutrient cycling and dissolved organic carbon dynamics. Here, we address the dependence of soil solution chemistry on disturbance regime using a novel combination of both experimental and observational results collected over a period of 16 years in montane tropical sites in the Luquillo Experimental Forest of Puerto Rico. Soil solution was sampled following various combinations of canopy trimming and detrital manipulation (2004), repeated manipulation (2014), drought (2015), and Hurricane Maria (2017). Soil solution was sensitive to disturbance but resilient, with return to baseline after 12–18 months. Any disturbance regime that involved loss of canopy and detrital inputs to the forest floor resulted in increased nitrate concentrations, but the response declined with repeated disturbance. Lysimeters in plots that had received no experimental manipulation had 1.5 times higher response to Hurricane Maria than those previously manipulated. The response to disturbance thus showed clear context dependence, with disturbance history affecting disturbance response. Among the nutrients and major ions, only nitrate showed a response to experimental manipulations, drought, and Hurricane Maria. In contrast to nitrate, soil solution potassium was unaltered by initial experimental manipulation but increased dramatically following drought and Hurricane Maria. Phosphorus only increased following Hurricane Maria and only in plots that had twice received experimental trimming and deposition of cut branches on the forest floor. Stoichiometry of dissolved organic matter also changed in these plots, with decreased carbon to nitrogen ratios. The potassium response suggests that damage to roots from tropical cyclones and drought is an important driver of the biogeochemical response to tropical storms. Dampening of soil nitrogen losses and increases in phosphorus losses following successive disturbance events indicates that increased frequency of tropical storms and droughts will result in fundamental alteration of soil biogeochemical cycles, with uncertain effects on forest structure.

Pyrogenic organic matter as a nitrogen source to microbes and plants following fire in an Arctic heath tundra

In recent years, wildfire frequency and severity has increased in the Arctic tundra regions due to climate change. Pyrogenic organic matter (PyOM) is a product of incomplete combustion of biomass containing nutrients such as nitrogen (N), and is expected to affect ecosystem N cycling during a post-fire recovery period. We investigated effects of fire on soil biogeochemical cycles with a focus on pyrogenic N turnover over two subsequent growing seasons, combined with and without summer warming, in an Arctic heath tundra, West Greenland. The summer warming was achieved by deployment of open top chambers (OTCs). We simulated an in situ tundra fire by removing vegetation and litter, and scorching/heating soil surface followed by the addition of 15N-labelled PyOM (derived from aboveground biomass and litter) to the soil surface in plots with and without summer warming. A darker surface after the simulated fire resulted in an increase of 1.3 °C in soil temperature at 5-cm depth over the growing seasons. The fire also caused a nine-fold increase in soil NH4+-N and three-fold increase in soil NO3−-N concentrations at 7-cm depth after two years. Tracing the fate of 15N-labelled PyOM, 21 days after its application, showed low 15N recovery in microbial biomass (0.4%) and total dissolved N (TDN) pools (0.01%). Microbial and root 15N recovery increased two-fold and 15-fold after one year, respectively, and TDN 15N recovery increased two-fold after two years, suggesting that relatively recalcitrant N of PyOM can be partly transformed into plant-available forms over time. Root and TDN 15N recovery was also significantly higher after two years of summer warming than under ambient temperature conditions, suggesting that summer warming can enhance availability of PyOM-N for recovering plants after the fire. Hence, we conclude that fire-induced PyOM can act as an N source for plant recovery in this Arctic tundra ecosystem for years after the fire, and this N source will become increasingly important in a future warmer climate.

Adaptation of soil micro-food web to elemental limitation: evidence from the forest-steppe ecotone

Stoichiometric imbalance between resources and their decomposers can alter the activity and structure of soil microbial communities and play an important role in regulating nutrient and carbon cycling in terrestrial ecosystems. However, whether and how ecological networks of soil micro-food web change to cope with the stoichiometric imbalance has never been assessed so far. In this study, we tested how the soil micro-food web responded to elemental limitations along a forest-steppe ecotone. We measured several adaptation mechanisms including soil microbial stoichiometry, enzyme activities and the composition of soil microbial and nematode communities. The microbial investment in resource acquisition shifted from nutrient-to C-acquiring enzymes with decreasing soil C:N:P ratios along the forest-steppe ecotone. The shifts in element use efficiencies could be a compensatory way besides enzyme allocation, implemented by microbial communities to cope with stoichiometric imbalance in their substrates. The community structure of soil micro-food web also changed with a decrease in saprotrophic fungi and fungivorous nematodes from the steppe plots towards the forest plots. The co-occurrence networks were less complex and stable with decreasing soil C:N:P ratios, suggesting that trophic interactions were less diverse and C-limitation plays an important role in structuring ecological interactions in soil food webs. Our findings provide insights into how stoichiometric constraints may induce shifts in ecological networks and have important implications for integrating shifts in individual physiological metabolism as well as changes in community composition of soil biota and to better understand and predict soil biogeochemical cycling in terrestrial ecosystems.

Responses of Biocrust and Associated Soil Bacteria to Novel Climates Are Not Tightly Coupled.

Climate change is expanding drylands even as land use practices degrade them. Representing ∼40% of Earth’s terrestrial surface, drylands rely on biological soil crusts (biocrusts) for key ecosystem functions including soil stability, biogeochemical cycling, and water capture. Understanding how biocrusts adapt to climate change is critical to understanding how dryland ecosystems will function with altered climate. We investigated the sensitivity of biocrusts to experimentally imposed novel climates to track changes in productivity and stability under both warming and cooling scenarios. We established three common gardens along an elevational-climate gradient on the Colorado Plateau. Mature biocrusts were collected from each site and reciprocally transplanted intact. Over 20 months we monitored visible species composition and cover, chlorophyll a, and the composition of soil bacterial communities using high throughput sequencing. We hypothesized that biocrusts replanted at their home site would show local preference, and biocrusts transplanted to novel environments would maintain higher cover and stability at elevations higher than their origin, compared to at elevations lower than their origin. We expected responses of the visible biocrust cover and soil bacterial components of the biocrust community to be coupled, with later successional taxa showing higher sensitivity to novel environments. Only high elevation sourced biocrusts maintained higher biocrust cover and community stability at their site of origin. Biocrusts from all sources had higher cover and stability in the high elevation garden. Later successional taxa decreased cover in low elevation gardens, suggesting successional reversal with warming. Visible community composition was influenced by both source and transplant environment. In contrast, soil bacterial community composition was not influenced by transplant environments but retained fidelity to the source. Thus, responses of the visible and soil bacterial components of the biocrust community were not coupled. Synthesis: Our results suggest biocrust communities are sensitive to climate change, and loss of species and function can be expected, while associated soil bacteria may be buffered against rapid change.

Earthworms exert long lasting afterlife effects on soil microbial communities

Earthworms dominate the invertebrate biomass in soils. Although the effects of living earthworms on soil functioning have been extensively studied, the ecological impacts of earthworm cadavers on soil microbiota remain unclear. In a 10-weeks laboratory incubation experiment, we monitored the influence of decomposing earthworm cadavers on the diversity and composition of soil bacterial, fungal and protistan communities. We found that the decomposition of earthworm cadavers decreased alpha diversity and changed the composition of microbial communities in comparison to control soil and soil with living earthworms. Although the functional composition of bacterial communities was not significantly influenced by the presence of dead earthworms, both fungal and protistan communities significantly shifted toward r-selected copiotrophic strategists; fungal communities were significantly enriched in molds and yeasts while protistan communities were enriched in saprotrophs. Our results suggest that dead earthworms play a distinct role in influencing soil microbial communities and associated functioning compared to their living counterparts. They further highlight that there is an increasing need to consider the afterlife effects of soil biota to better predict soil biogeochemical cycling in terrestrial ecosystems.

Microbial nutrient limitation and catalytic adjustments revealed from a long‐term nutrient restriction experiment

AbstractIntroductionMicrobial abundance and activities in soils are predominantly determined by soil carbon (C), nitrogen (N) and phosphorus (P) availability. Much research has focused on the effects of soil N than P availability on soil microbial biomass and enzyme activities as sensitive proxies of microbial ecophysiology highlighting the need to investigate how microbes will respond to P availability in soil, especially in cropping systems.Materials and MethodsThe effect of P fertilisation on microbial biomass‐C, ‐N and ‐P, and the kinetic parameters (maximal velocity [Vmax], Michaelis constant [Km] and catalytic efficiency [Ka]) of β‐1,4‐glucosidase (BG; C‐acquiring), leucine‐aminopeptidase (LAP; predominantly N‐acquiring) and acid phosphomonoesterase (PHO; P‐acquiring) were measured in a nutrient‐poor agricultural soil (devoid of fertiliser application since 1942).ResultsThis study showed that P fertilisation led to a 65% and 56% increase in microbial biomass‐N and ‐P, respectively, indicating severe P limitation and inefficient N acquisition by microbes without P availability. Increased Ka values of LAP with P fertilisation further hint toward the production of efficient isoenzymes to avoid resource tradeoffs for nutrient acquisition.ConclusionsOverall, these results decipher microbial metabolic and catalytic adjustments mediated by soil P availability. Increased microbial biomass‐N and ‐P with P fertilisation indicated microbial N and P colimitation that was partly overcome by the production of efficient enzymes for N acquisition with P fertilisation. We argue to incorporate microbial enzyme activities as a response to different management strategies to better inform us about soil biogeochemical cycles in cropping systems.

Biochemical composition and function of subalpine shrubland and meadow soil microbiomes in the Qilian Mountains, Qinghai-Tibetan plateau, China.

Microorganisms participate in the soil biogeochemical cycle. Therefore, investigating variations in microbial biomass, composition, and functions can provide a reference for improving soil ecological quality due to the sensitivity of microorganisms to vegetation coverage changes. However, the differences in soil microorganisms between shrubland and meadow have not been investigated in ecologically vulnerable subalpine areas. This study aimed to investigate the biochemical composition and functions of the soil microbial community under two shrublands and a meadow at high altitudes (3,400–3,550 m). Three sites under two shrublands, Rhododendron thymifolium (RHO) and Potentilla fruticosa (POT), and one meadow dominated by Kobresia myosuroides (MEA), were selected on the southern slope of the Qilian Mountains on the northeastern edge of the Qinghai–Tibetan Plateau, China. Soil physicochemical properties, the microbial community composition expressed by the phospholipid fatty acid (PLFA) biomarker, and enzyme activities were analyzed as well as their relationships. The results showed that water holding capacity and the soil carbon, nitrogen, and potassium content in RHO and POT were higher than those in the MEA. Moreover, the soil active carbon, dissolved organic carbon, total nitrogen, and dissolved total nitrogen content in RHO were higher than those in POT. The abundance of total PLFAs, bacteria, and fungi beneath the shrublands was considerably higher than that in the MEA. The PLFA abundance in RHO was significantly higher than that in POT. The fungal-to-bacterial ratio of RHO and POT was significantly higher than that in the MEA. The activities of β-glucosidase, cellobiohydrolase, and leucine aminopeptidase were the highest in RHO among the three vegetation types, followed by POT and MEA. The redundancy analysis indicated that the biochemical composition of the soil microorganisms and enzyme activities were driven by total nitrogen, dissolved organic carbon, water holding capacity, and soil organic carbon. Therefore, shrublands, which have higher biomass, can improve soil moisture status, increase soil carbon and nitrogen content (especially active carbon and active nitrogen), and further increase the abundance of total PLFAs, bacteria, and fungi. The increase of microbial biomass indirectly enhances the activity of relevant soil enzymes. The variations in PLFA abundance and enzyme activities can be attributed to shrub species, especially evergreen shrubs, which create more favorable conditions for soil microorganisms. This study provides a theoretical basis for investigating the soil biogeochemical cycle and a scientific basis for soil management and vegetation restoration in the subalpine regions.

Spectral characteristics of dissolved organic matter and its environmental responses across successional stages in a glacier retreat area

Dissolved organic matter (DOM), the most active type of soil organic matter, plays a key role in soil biogeochemical cycling. Therefore, exploring the source, composition, environmental response, and accumulation mechanism of DOM during vegetation succession has great significance for predicting soil carbon cycling. In this study, DOM was extracted from topsoil and subsoil at plots after 12, 30, 40, 50, 80, and 120 years of primary succession along the Hailuogou Glacier retreat area. The concentrations and spectral characteristics of DOM were analyzed via a combination of elemental analysis, ultraviolet-visible spectroscopy, and three-dimensional fluorescence excitation-emission matrix spectroscopy. The results showed that concentrations of soil dissolved organic carbon and dissolved organic nitrogen of both topsoil and subsoil increased significantly during vegetation succession. Along the chronosequence, the protein-like components and optical indices were significantly enhanced, humic-like components and the optical indices decreased, the aromaticity degree of DOM increased first and then decreased. Soil pH and NH4+-N content explained 62.2% of the total variation of surface soil DOM components, while soil moisture and pH explained 64.3% of that of subsurface soil DOM, indicating that environmental conditions were key factors affecting the concentrations and composition of soil DOM in the Hailuogou Glacier retreat area.

Grazing Effects of Soil Fauna on White-Rot Fungi: Biomass, Enzyme Production and Litter Decomposition Ability.

Soil invertebrates and microorganisms are two major drivers of litter decomposition. Even though the importance of invertebrates and microorganisms in biogeochemical soil cycles and soil food webs has been studied, the effects of invertebrates on fungi are not well understood compared to other organisms. In this work, we investigated the effects of soil invertebrates on fungi as a factor that cannot be ignored in the study of nutrient cycling. The result showed the grazing of isopods on white-rot fungi was transitive and persistent. The grazed fungi appeared “compensatory” growing. The biomass of fungi increased after grazing. The activities of enzymes associated with nutrient cycling were increased under grazing. The zymography images showed the enzyme hotspots and activities also increased significantly in the grazing area. The results suggest that invertebrate grazing can significantly increase the fungal biomass and enzyme activity, accelerating litter decomposition in the unreached grazer area. The grazing effects of invertebrate plays an important role in promoting the nutrient cycling of the forest ecosystem. We believe that this study will be a good reference related to showing the relationship between soil invertebrates, fungi and soil biogeochemical cycles.