Light structures phototroph, bacterial and fungal communities at the soil surface

Unraveling microbial processes involved in carbon and nitrogen cycling and greenhouse gas emissions in rewetted peatlands by molecular biology

Restoration of drained peatlands through rewetting has recently emerged as a prevailing strategy to mitigate excessive greenhouse gas emissions and re-establish the vital carbon sequestration capacity of peatlands. Rewetting can help to restore vegetation communities and biodiversity, while still allowing for extensive agricultural management such as paludiculture. Belowground processes governing carbon fluxes and greenhouse gas dynamics are mediated by a complex network of microbial communities and processes. Our understanding of this complexity and its multi-factorial controls in rewetted peatlands is limited. Here, we summarize the research regarding the role of soil microbial communities and functions in driving carbon and nutrient cycling in rewetted peatlands including the use of molecular biology techniques in understanding biogeochemical processes linked to greenhouse gas fluxes. We emphasize that rapidly advancing molecular biology approaches, such as high-throughput sequencing, are powerful tools helping to elucidate the dynamics of key biogeochemical processes when combined with isotope tracing and greenhouse gas measuring techniques. Insights gained from the gathered studies can help inform efficient monitoring practices for rewetted peatlands and the development of climate-smart restoration and management strategies.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10533-024-01122-6.

Effects of nursery production methods on fungal community diversity within soil and roots of Abies alba Mill

The aim of this study was to elucidate how different nursery production methods influence the composition of and relationship between soil and root community levels of Abies alba. In the Międzylesie Forest District, we quantified the responses of samples of both community-level fine roots and surrounding soil to environmental changes evoked by various seedling production methods. Fungi levels were identified based on their ITS 1 region and 5.8 S rDNA component. Analysis was conducted using Illumina SBS technology, and the obtained sequences were compared with reference samples deposited in the UNITE. Chemical analysis of the soil was also performed. Different nursery production methods resulted in a strong decoupling in the responses of fungal community levels between soil and roots. Changes in growth conditions imposed by production methods were significant in determining species composition. We found differences in fungal communities among functional groups of samples. In the soil, the dominant species of mycorrhizal fungi were Tylospora asterophora, Amanita rubescens, and Russula ionochlora. Mycorrhizal fungi in roots included Tuber anniae, Thelephoraceae sp., and Acephala applanata. Specific soil substrate conditions significantly influenced fungal community composition, leading to an increase in abundance of mycorrhizal fungi, specifically T. anniae.

Improved assessment of the impacts of plant protection products on certain soil ecosystem services requires better consideration of terrestrial microalgae and cyanobacteria

There is growing scientific and societal consciousness that the environmental risks and impacts of plant protection products (PPPs) cannot be properly assessed without considering ecosystem services. However, the science on this issue remains incomplete and fragmented, as recently illustrated in a collective scientific assessment that pointed out the limited knowledge on the risks and impacts of PPPs on soil ecosystem services, which are clearly overlooked. Beside soil ecosystem services, certain key players involved in these services are largely overlooked in the scientific literature on the risks and impacts of PPPs, namely soil microbial photosynthetic communities. Here, we followed the principles of evidence-based logic chain approaches to show the importance of considering these microorganisms when studying the impacts of PPPs on certain services provided by soil ecosystems, with a focus on regulating and maintenance services that play a role in the regulation of baseline flows and extreme events. Terrestrial microalgae and cyanobacteria are ubiquitous photosynthetic microorganisms that, together with other soil micro- and macro-organisms, play key roles in the ecosystem functions that underpin these ecosystem services. There is an extensive literature on the ecotoxicological effects of PPPs on different organisms including soil microorganisms, but studies concerning soil microbial photosynthetic communities are very scarce. However, there is scientific evidence that herbicides can have both direct and indirect impacts on these microbial photosynthetic communities. Given that they play key functional roles, we argue that soil microbial photosynthetic communities warrant greater attention in efforts to assess the environmental risks and impacts of PPPs and, ultimately, help preserve or restore the regulating and maintenance services provided by soil ecosystems.

Dynamics of vanadium and response of inherent bacterial communities in vanadium-titanium magnetite tailings to beneficiation agents, temperature, and illumination

Vanadium-titanium (V-Ti) magnetite tailings contain toxic metals that could potentially pollute the surrounding environment. However, the impact of beneficiation agents, an integral part of mining activities, on the dynamics of V and the microbial community composition in tailings remains unclear. To fill this knowledge gap, we compared the physicochemical properties and microbial community structure of V-Ti magnetite tailings under different environmental conditions, including illumination, temperature, and residual beneficiation agents (salicylhydroxamic acid, sodium isobutyl xanthate, and benzyl arsonic acid) during a 28-day reaction. The results revealed that beneficiation agents exacerbated the acidification of the tailings and the release of V, among which benzyl arsonic acid had the greatest impact. The concentration of soluble V in the leachate of tailings with benzyl arsonic acid was 6.4 times higher than that with deionized water. Moreover, illumination, high temperatures, and beneficiation agents contributed to the reduction of V in V-containing tailings. High-throughput sequencing revealed that Thiobacillus and Limnohabitans adapted to the tailings environment. Proteobacteria was the most diverse phylum, and the relative abundance was 85.0%-99.1%. Desulfovibrio, Thiobacillus, and Limnohabitans survived in the V-Ti magnetite tailings with residual beneficiation agents. These microorganisms could contribute to the development of bioremediation technologies. The main factors affecting the diversity and composition of bacteria in the tailings were Fe, Mn, V, SO₄^2-, total nitrogen, and pH of the tailings. Illumination inhibited microbial community abundance, while the high temperature (39.5 °C) stimulated microbial community abundance. Overall, this study strengthens the understanding of the geochemical cycling of V in tailings influenced by residual beneficiation agents and the application of inherent microbial techniques in the remediation of tailing-affected environments.

Building a Conceptual Model for the Environmental Fate of the Fungicide Benzovindiflupyr

Degradation of the fungicide benzovindiflupyr was slow in standard regulatory laboratory studies in soil and aquatic systems, suggesting it is a persistent molecule. However, the conditions in these studies differed significantly from actual environmental conditions, particularly the exclusion of light, which prevents potential contributions from the phototrophic microorganisms that are ubiquitous in both aquatic and terrestrial environments. Higher tier laboratory studies that include a more comprehensive range of degradation processes can more accurately describe environmental fate under field conditions. Indirect aqueous photolysis studies with benzovindiflupyr showed that the photolytic half-life in natural surface water can be as short as 10 days, compared with 94 days in pure buffered water. Inclusion of a light-dark cycle in higher tier aquatic metabolism studies, to include the contribution of phototrophic organisms, reduced the total system half-life from >1 year in dark test systems to as little as 23 days. The relevance of these additional processes was confirmed in an outdoor aquatic microcosm study in which the half-life of benzovindiflupyr was 13-58 days. In laboratory soil degradation studies, the degradation rate of benzovindiflupyr was significantly faster in cores with an undisturbed surface microbiotic crust, incubated in a light-dark cycle (half-life of 35 days), than in regulatory studies with sieved soil in the dark (half-life >1 year). A radiolabeled field study validated these observations, showing residue decline with a half-life of approximately 25 days over the initial 4 weeks. Conceptual models of environmental fate based on standard regulatory studies may be incomplete, and additional higher tier laboratory studies can be valuable in elucidating degradation processes and improving the prediction of persistence under actual use conditions. Environ Toxicol Chem 2023;42:995-1009. © 2023 SETAC.

Nutrient loading decreases blue carbon by mediating fungi activities within seagrass meadows

Coastal pollution, including nutrient loading, can negatively impact seagrass health and cover and may consequently alter soil organic carbon (SOC) accumulation and preservation. Key to understanding how eutrophication impacts SOC cycling in seagrass ecosystems is how nutrient loading changes the sources of carbon being deposited and how these changes in resources, both nutrients and carbon availability, influence soil microbiota community and activity. Currently, the direction and magnitude of nutrient loading impacts on seagrass SOC dynamics are poorly understood at a meadow scale, limiting our ability to reveal the driving mechanisms of SOC remineralisation. The purpose of this study was to assess the response of surface SOC and soil microbiomes to nutrient loading within tropical seagrass meadows. To achieve this, we quantified both total SOC and recalcitrant soil organic carbon (RSOC) concentrations and sources, in addition to the composition of bacterial and fungal communities and soil extracellular enzyme activities. We found that nutrient loading elevated SOC and RSOC content, mainly facilitated by enhanced algal growth. There was no nutrient effect on the soil prokaryotic communities, however, saprotrophic fungi groups (i.e. Trapeliales, Sordaridales, Saccharomycetales and Polyporales) and fungal activities were elevated under high nutrient conditions, including extracellular enzyme activities linked to seagrass-based cellulose and lignin decomposition. This relative increase in RSOC transformation may decrease the relative contribution of seagrass carbon to RSOC pools. Additionally, significantly different fungal communities were observed between adjacent T. hemprichii and E. acoroides areas, which coincided with elevated RSOC-decomposing enzyme activity in T. hemprichii meadows, even though the mixed seagrass meadow received allochthonous SOC and RSOC from the same sources. These results suggest that nutrient loading stimulated fungal activity and community shifts specific to the local seagrass species, thereby causing fine-scale (within-meadow) variability in SOC cycling in response to nutrient loading. This study provides evidence that fungal composition and activity, mediated by human activities (e.g. nutrient loading), can be an important influence on seagrass blue carbon accumulation and remineralisation.

Soil Depth Significantly Shifted Microbial Community Structures and Functions in a Semiarid Prairie Agroecosystem

The North American Great Plains cover a large area of the Nearctic ecozone, and an important part of this biome is semiarid. The sustainable intensification of agriculture that is necessary to produce food for an ever-increasing world population requires knowledge of the taxonomic and functional structure of the soil microbial community. In this study, we investigated the influence of soil depth on the composition and functions of the microbial communities hosted in agricultural soils of a semiarid agroecosystem, using metagenomic profiling, and compared them to changes in soil chemical and physical properties. Shotgun sequencing was used to determine the composition and functions of the soil microbial community of 45 soil samples from three soil depths (0-15 cm, 15-30 cm, and 30-60 cm) under different agricultural land use types (native prairie, seeded prairie, and cropland) in southwest Saskatchewan. Analysis of community composition revealed the declining abundance of phyla Verrucomicrobia, Bacteroidetes, Chlorophyta, Bacillariophyta, and Acidobacteria with soil depth, whereas the abundance of phyla Ascomycota, Nitrospirae, Planctomycetes, and Cyanobacteria increased with soil depth. Soil functional genes related to nucleosides and nucleotides, phosphorus (P) metabolism, cell division and cell cycle, amino acids and derivatives, membrane transport, and fatty acids were particularly abundant at 30-60 cm. In contrast, functional genes related to DNA and RNA metabolism, metabolism of nitrogen, sulfur and carbohydrates, and stress response were more abundant in the top soil depth. The RDA analysis of functional genes and soil physico-chemical properties revealed a positive correlation between phages and soil organic P concentrations. In the rooting zone of this semiarid agroecosystem, soil microbes express variable structural patterns of taxonomic and functional diversity at different soil depths. This study shows that the soil microbial community is structured by soil depth and physicochemical properties, with the middle soil depth being an intermediate transition zone with a higher taxonomic diversity. Our results suggest the co-existence of various microbial phyla adapted to upper and lower soil depths in an intermediate-depth transition zone.

The Impact of Disturbed Soil Structure on the Degradation of 2 Fungicides Under Constant and Variable Moisture

Degradation of agrochemicals in soil is frequently faster under field conditions than in laboratory studies. Field studies are carried out on relatively undisturbed soil, whereas laboratory studies typically use sieved soil, which can have a significant impact on the physical and microbial nature of the soil and may contribute to differences in degradation between laboratory and field studies. A laboratory study was therefore conducted to determine the importance of soil structure and variable soil moisture on the degradation of 2 fungicides (azoxystrobin and paclobutrazol) that show significant differences between laboratory and field degradation rates in regulatory studies. Degradation rates were measured in undisturbed cores of a sandy clay loam soil (under constant or variable moisture contents) and in sieved soil. For azoxystrobin, degradation rates under all conditions were similar (median degradation time [DegT50] 34-37 d). However, for paclobutrazol, degradation was significantly faster in undisturbed cores (DegT50 255 d in sieved soil and 63 d in undisturbed cores). Varying the moisture content did not further enhance degradation of either fungicide. Further examination into the impact of soil structure on paclobutrazol degradation, comparing undisturbed and sieved/repacked cores, revealed that the impact of sieving could not be mitigated by repacking the soil to a realistic bulk density. Examination of fungal and bacterial community structure using automated ribosomal spacer analysis showed significant initial differences between sieved/repacked and intact soil cores, although such differences were reduced at the end of the study (70 d). The present study demonstrates that disruption of soil structure significantly impacts microbial community structure, and for some compounds this may explain the differences between laboratory and field degradation rates. Environ Toxicol Chem 2021;40:2715-2725. © 2021 SETAC.

Inclusion of seasonal variation in river system microbial communities and phototroph activity increases environmental relevance of laboratory chemical persistence tests

Regulatory tests assess crop protection product environmental fate and toxicity before approval for commercial use. Although globally applied laboratory tests can assess biodegradation, they lack environmental complexity. Microbial communities are subject to temporal and spatial variation, but there is little consideration of these microbial dynamics in the laboratory. Here, we investigated seasonal variation in the microbial composition of water and sediment from a UK river across a two-year time course and determined its effect on the outcome of water-sediment (OECD 308) and water-only (OECD 309) biodegradation tests, using the fungicide isopyrazam. These OECD tests are performed under dark conditions, so test systems incubated under non-UV light:dark cycles were also included to determine the impact on both inoculum characteristics and biodegradation. Isopyrazam degradation was faster when incubated under non-UV light at all collection times in water-sediment microcosms, suggesting that phototrophic communities can metabolise isopyrazam throughout the year. Degradation rate varied seasonally between inoculum collection times only in microcosms incubated in the light, but isopyrazam mineralisation to ¹⁴CO₂ varied seasonally under both light and dark conditions, suggesting that heterotrophic communities may also play a role in degradation. Bacterial and phototroph communities varied across time, but there was no clear link between water or sediment microbial composition and variation in degradation rate. During the test period, inoculum microbial community composition changed, particularly in non-UV light incubated microcosms. Overall, we show that regulatory test outcome is not influenced by temporal variation in microbial community structure; however, biodegradation rates from higher tier studies with improved environmental realism, e.g. through addition of non-UV light, may be more variable. These data suggest that standardised OECD tests can provide a conservative estimate of pesticide persistence end points and that additional tests including non-UV light could help bridge the gap between standard tests and field studies.

Variance in bacterial communities, potential bacterial carbon sequestration and nitrogen fixation between light and dark conditions under elevated CO2 in mine tailings

This study is the first to show the response of bacterial communities with primary carbon and nitrogen fixers to elevated CO₂ (eCO₂) in light and dark conditions based on 6 months of culture growth. Carbon sequestration and nitrogen fixation were analyzed by ¹³C and ¹⁵N isotope labeling using ¹³C-labeled CO₂ and ¹⁵N-labeled N₂, followed by pyrosequencing and DNA-based stable isotope probing (SIP) to identify carbon fixers and nitrogen fixers. The results indicated that eCO₂ decreased the Chao 1 richness, and the eCO₂-light treatment exhibited the highest Shannon diversity. In addition, eCO₂ (in either light or dark conditions) greatly increased the relative abundances of bacteria belonging to the classes Betaproteobacteria and Alphaproteobacteria. The ¹³C atom % in the mine tailings increased from 1.108 to 1.84 ± 0.11 under light conditions and 1.52 ± 0.17 under dark conditions after 6 months of culture growth. Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) form I-coding gene (cbbL) copy numbers were 164.30-fold and 40.36-fold higher than RubisCO form II-coding gene (cbbM) copy numbers in the heavy fractions with a buoyant density of 1.7388 g·mL^-1 relative to the buoyant density gradients of DNA fractions obtained under eCO₂-light and eCO₂-dark treatment, respectively. The Proteobacteria-like cbbL genes were dominant in the carbon fixers. In addition, the ¹⁵N atom % in the mine tailings increased from 0.366 to 0.454 ± 0.021 in light conditions and 0.437 ± 0.018 in dark conditions. Furthermore, uncultured nitrogen-fixing bacteria were the dominant nitrogen fixers in light conditions, and bacteria harboring the Bradyrhizobium-like nifH and Leptospirillum-like nifH genes were the dominant nitrogen fixers in dark conditions. These first data for a mine tailing ecosystem are inconsistent with those obtained for a range of other ecosystems, in which the effects of CO₂ were limited to several nonphotoautotrophic communities and different nitrogen fixers.

Microbial Nursery Production of High-Quality Biological Soil Crust Biomass for Restoration of Degraded Dryland Soils

Biological soil crusts (biocrusts) are slow-growing, phototroph-based microbial assemblages that develop on the topsoils of drylands. Biocrusts help maintain soil fertility and reduce erosion. Because their loss through human activities has negative ecological and environmental health consequences, biocrust restoration is of interest. Active soil inoculation with biocrust microorganisms can be an important tool in this endeavor. We present a culture-independent, two-step process to grow multispecies biocrusts in open greenhouse nursery facilities, based on the inoculation of local soils with local biocrust remnants and incubation under seminatural conditions that maintain the essence of the habitat but lessen its harshness. In each of four U.S. Southwest sites, we tested and deployed combinations of factors that maximized growth (gauged as chlorophyll a content) while minimizing microbial community shifts (assessed by 16S rRNA sequencing and bioinformatics), particularly for crust-forming cyanobacteria. Generally, doubling the frequency of natural wetting events, a 60% reduction in sunlight, and inoculation by slurry were optimal. Nutrient addition effects were site specific. In 4 months, our approach yielded crusts of high inoculum quality reared on local soil exposed to locally matched climates, acclimated to desiccation, and containing communities minimally shifted in composition from local ones. Our inoculum contained abundant crust-forming cyanobacteria and no significant numbers of allochthonous phototrophs, and it was sufficient to treat ca. 6,000 m2 of degraded dryland soils at 1 to 5% of the typical crust biomass concentration, having started from a natural crust remnant as small as 6 to 30 cm2 IMPORTANCE: Soil surface crusts can protect dryland soils from erosion, but they are often negatively impacted by human activities. Their degradation causes a loss of fertility, increased production of fugitive dust and intensity of dust storms with associated traffic problems, and provokes general public health hazards. Our results constitute an advance in the quest to actively restore biological soil covers by providing a means to obtain high-quality inoculum within a reasonable time (a few months), thereby allowing land managers to recover essential, but damaged, ecosystem services in a sustainable, self-perpetuating way as provided by biocrust communities.